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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/phast">Debian Med / phast</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/phast/commit/68bd3b9c9776d5718adf3b0d35043beec979ed04">68bd3b9c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-18T16:20:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix homepage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phast/commit/b8561ed0e11ac5881daff1b5f566ea558d974be3">b8561ed0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-18T16:21:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update d/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phast/commit/a8529b20d78d8cff56f2a433f6571b0712f829d1">a8529b20</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-18T16:21:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phast/commit/67cfb1e78fc7f1ec1f7b580942a0e2d41ba3cdb9">67cfb1e7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-18T16:21:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phast/commit/0af533bddd68163b7f6e9ef7d46ba457cb3d3bbc">0af533bd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-18T16:21:42Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phast/commit/dc8ace42d8c5bd614524c80419e03908d23800ed">dc8ace42</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-18T16:55:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run part of the test suite
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/phast/commit/822eeb78bd8e0aad96f9bc37b929a24d47ef01dd">822eeb78</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-18T17:33:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run tests
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</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="#05fd7a89568710df125a7ec0ed121d2fb9d96e4d">
<span class="new-file">
+
debian/patches/fix_test_makefile.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</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/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">phast (1.4+dfsg-2) UNRELEASED; urgency=medium</span>
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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"> * Fix homepage</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"> * debhelper 11</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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(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="LC7" class="line" lang="plaintext"> * Run part or the test suite</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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 18 Oct 2018 18:16:40 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">phast (1.4+dfsg-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="plaintext"> * Initial release (Closes: #875555)</span>
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<br>
</li>
<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,16 +3,16 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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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="LC4" class="line" lang="plaintext">Section: science</span>
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<td class="diff-line-num new_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">
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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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">0</span>),</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>),</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> liblapack-dev,</span>
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<td class="diff-line-num 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">
8
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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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libblas-dev,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libtmglib-dev,</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libpcre3-dev,</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> help2man</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.0</span></span>
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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
13
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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/phast.gi</span>t</span>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/phast.git</span>
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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
15
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<td class="diff-line-num new_line old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Homepage: http://compgen.cshl<span class="idiff left right">/edu/phast</span></span>
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<td class="diff-line-num new old_line" data-linenumber="16" style="width: 35px; color: rgba(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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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/phas</span>t</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/phast.git</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Homepage: http://compgen.cshl<span class="idiff left right">.edu/phast/</span></span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Package: phast</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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<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">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Architecture: any</span>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: PHAST</span>
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3
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(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="LC3" class="line" lang="plaintext">Upstream-Contact: Ritika Ramani <rramani@cshl.edu></span>
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4
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Source: https://github.com/CshlSiepelLab/phast/releases</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,11 +9,11 @@ Comment: The file LICENSE.txt mentions Philip Hazel (University of Cambridge</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> the upstream source it is not mentioned here in this file.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Copyright: 2002-201<span class="idiff left right">5</span> University of California, Cornell University</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Copyright: 2002-201<span class="idiff left right">8</span> University of California, Cornell University</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Copyright: 2016 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Copyright: 2016<span class="idiff left right">-2018</span> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">License: BSD-3-clause</span>
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<li id="05fd7a89568710df125a7ec0ed121d2fb9d96e4d">
<a href="https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd#05fd7a89568710df125a7ec0ed121d2fb9d96e4d"><strong>debian/patches/fix_test_makefile.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Thu, 18 Oct 2018 18:16:40 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Test suite makefile has syntax errors and there</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> was at least one buggy data file which was fixed.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> With these changes `make msa_view` works but other targets are</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> throwing errors. This needs to be investigated</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/Makefile</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -7,30 +7,30 @@ all: msa_view phyloFit phastCons</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> msa_view:</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> @echo "*** Testing msa_view ***"</span>
</pre>
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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"> msa_view hmrc.ss -i SS --end 10000 > hmrc.fa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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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="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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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="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> msa_view hmrc.fa -o PHYLIP > hmrc.ph</span>
</pre>
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<td class="diff-line-num new new_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">
18
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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="LC18" class="line" lang="diff"> msa_view hmrc.ph -i PHYLIP > hmrc.fa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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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="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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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="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> msa_view hmrc.ph --out-format MPM --in-format PHYLIP > hmrc.mpm</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> msa_view hmrc.mpm --in-format MPM > hmrc.fa</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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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="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hmrc.fa hmrc_correct.fa` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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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="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hmrc.fa hmrc_correct.fa ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> msa_view hmrc.fa -o SS > hmrc_short_a.ss</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> msa_view hmrc.ss --end 10000 -i SS -o SS > hmrc_short_b.ss</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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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="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hmrc_short_[ab].ss` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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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="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hmrc_short_[ab].ss ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> msa_view --seqs human,cow hmrc_short_a.ss -i SS -o SS | msa_view - -i SS > hm_a.fa</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> msa_view --seqs human,cow hmrc.fa > hm_b.fa</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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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="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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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="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> msa_view hmrc.ss --gap-strip ANY -i SS -o SS | msa_view - -i SS > hmrc_nogaps_a.fa</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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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="LC34" class="line" lang="diff"> msa_view hmrc.ss -i SS | msa_view - --gap-strip ANY > hmrc_nogaps_b.fa</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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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="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hmrc_nogaps_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hmrc_nogaps_[ab].fa ; then echo "ERROR" ; exit 1 ; fi</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> msa_view hmrc.fa --seqs human,cow --gap-strip ALL > hm_a.fa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> msa_view hmrc_short_a.ss --seqs human,cow -i SS --gap-strip ALL > hm_b.fa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hm_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hm_[ab].fa ; then echo "ERROR" ; exit 1 ; fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> msa_view hmrc.ss --start 10000 --end 20000 -i SS > hmrc_sub_a.fa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> msa_view hmrc.ss -i SS | msa_view - --start 10000 --end 20000 > hmrc_sub_b.fa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hmrc_sub_[ab].fa` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief hmrc_sub_[ab].fa ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> msa_view hmrc.ss --summary -i SS > hmrc_summary</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief hmrc_summary hmrc_summary_correct` ]] ; then echo "ERROR" ; exit 1 ; fi</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;">+ if ! diff --brief -b hmrc_summary hmrc_summary_correct ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> @echo -e "Passed all tests.\n"</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> @rm -f hmrc.ph hmrc.fa hmrc.mpm hmrc_short_[ab].ss hm_[ab].fa hmrc_nogaps_[ab].fa hmrc_sub_[ab].fa hmrc_summary</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -43,40 +43,40 @@ msa_view:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> phyloFit:</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> @echo "*** Testing phyloFit ***"</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod JC69 --tree "(human, (mouse,rat), cow)" -i SS --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(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="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod jc.mod ; then echo "Rounding errors found" ; diff -u phyloFit.mod jc.mod ; fi</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod JC69 --tree "((((human,chimp), (mouse,rat)), cow), chicken)" -i SS --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" style="width: 35px; color: rgba(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="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod jc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod jc.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod F81 --tree "(human, (mouse,rat), cow)" -i SS --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod f81.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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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="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod f81.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --quiet</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod hky.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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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="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod hky.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --quiet</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod rev.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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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="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod rev.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod UNREST --tree "(human, (mouse,rat), cow)" -i SS --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod unrest.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod unrest.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">- @if [[ -n `diff --brief phyloFit.mod hky-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">+ if ! diff --brief phyloFit.mod hky-dg.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS -k 4 --quiet </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">- @if [[ -n `diff --brief phyloFit.mod rev-dg.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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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="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod rev-dg.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod HKY85 --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod hky-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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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="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod hky-em.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat), cow)" -i SS --EM --quiet</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod rev-em.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod rev-em.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> phyloFit hpmrc.ss --subst-mod REV --tree "(hg16, (mm3,rn3), galGal2)" -i SS --gaps-as-bases --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod rev-gaps.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod rev-gaps.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod REV -i SS --init-model rev.mod --post-probs --lnl --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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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="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod rev-lnl.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.postprob rev.postprob` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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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="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod rev-lnl.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.postprob rev.postprob ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod REV --tree "(human, (mouse,rat))" -i SS --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">- @if [[ -n `diff --brief phyloFit.mod rev-hmr.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">+ if ! diff --brief phyloFit.mod rev-hmr.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> msa_view hmrc.ss -i SS --seqs human,mouse,rat --unordered -o SS > hmr.ss</span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> phyloFit hmr.ss -i SS --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod rev-hmr2.mod` ]] ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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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="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod rev-hmr2.mod ; then echo "ERROR" ; exit 1 ; fi # FIXME: rev-hmr.mod and rev-hmr2.mod should be equal (eq freqs being obtained from all seqs)</span></span>
</pre>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> msa_view hmrc.ss -i SS --seqs human,mouse --unordered -o SS > hm.ss</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> phyloFit hm.ss -i SS --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod rev-hm.mod` ]] ; then echo "ERROR" ; exit 1 ; fi </span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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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="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod rev-hm.mod ; then echo "ERROR" ; exit 1 ; fi </span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> phyloFit hmrc.ss --subst-mod UNREST --tree "((human, mouse), cow)" -i SS --ancestor cow --quiet</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief phyloFit.mod unrest-cow-anc.mod` ]] ; then echo "ERROR" ; exit 1 ; fi</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief phyloFit.mod unrest-cow-anc.mod ; then echo "ERROR" ; exit 1 ; fi</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> @echo -e "Passed all tests.\n"</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> @rm -f phyloFit.mod phyloFit.postprob hmr.ss hm.ss</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"><span class="gu" style="color: #800080; font-weight: 600;">@@ -87,12 +87,12 @@ phyloFit:</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> phastCons:</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> @echo "*** Testing phastCons ***"</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> phastCons hpmrc.ss hpmrc-rev-dg-global.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements.bed --seqname chr22 > cons.dat</span>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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;">- @if [[ -n `diff --brief cons.dat cons_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi </span></span>
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<td class="diff-line-num new new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief elements.bed elements_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi </span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief cons.dat cons_correct.dat ; then echo "ERROR" ; exit 1 ; fi </span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief elements.bed elements_correct.bed ; then echo "ERROR" ; exit 1 ; fi </span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> tree_doctor hpmrc-rev-dg-global.mod --prune galGal2 > hpmr.mod</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> phastCons hpmrc.ss hpmr.mod --nrates 20 --transitions .08,.008 --quiet --viterbi elements-4way.bed --seqname chr22 > cons-4way.dat</span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief cons-4way.dat cons-4way_correct.dat` ]] ; then echo "ERROR" ; exit 1 ; fi </span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @if [[ -n `diff --brief elements-4way.bed elements-4way_correct.bed` ]] ; then echo "ERROR" ; exit 1 ; fi </span></span>
</pre>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief cons-4way.dat cons-4way_correct.dat ; then echo "ERROR" ; exit 1 ; fi </span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ! diff --brief elements-4way.bed elements-4way_correct.bed ; then echo "ERROR" ; exit 1 ; fi </span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> @echo -e "Passed all tests.\n"</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> @rm -f cons.dat cons-4way.dat elements.bed elements-4way.bed hpmr.mod</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -110,7 +110,7 @@ phyloP:</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> phyloP --null 10 phyloFit.mod > phyloP_null_test.txt</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> phyloP -i SS phyloFit.mod hmrc.ss > phyloP_sph_test.txt</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> phyloP -i SS --method LRT phyloFit.mod hmrc.ss > phyloP_lrt_test.txt</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ phyloP -i SS --method LRT --mode CONACC phyloFit.mod hmrc.ss > phyloP_lrt_conacc_test.txt</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> phyloP -i SS --method GERP phyloFit.mod hmrc.ss > phyloP_gerp_test.txt</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> phyloP -i SS --method SCORE phyloFit.mod hmrc.ss > phyloP_score_test.txt</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> phyloP -i SS --method LRT --wig-scores phyloFit.mod hmrc.ss > phyloP_wig_test.wig</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/test/hmrc_summary_correct</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/test/hmrc_summary_correct</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,5 +1,2 @@</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-descrip. A C G T G+C length all_gaps some_gaps</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> descrip. A C G T G+C length all_gaps some_gaps</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> hmrc.ss 0.3258 0.1913 0.1827 0.3001 0.3740 95927 0 82185</span></pre>
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<a href="https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,3 +3,4 @@ do_not_install_to_opt.patch</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">use_debian_packaged_libpcre.patch</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">use_debian_packaged_help2man.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">hardening.patch</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">fix_test_makefile.patch</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/phast/compare/91738c65ddbc5547a11cb099b8f29e831f254103...822eeb78bd8e0aad96f9bc37b929a24d47ef01dd#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -10,3 +10,8 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all</td>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">override_dh_auto_clean:</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> cd src && make clean</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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="plaintext">override_dh_auto_test:</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> cd test && PATH=$(CURDIR)/bin:$(PATH) make msa_view</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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">endif</span></pre>
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