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<h3>
Michael R. Crusoe pushed to branch master
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/d5618e5a7ce9841e342b875cbf61f8d38c5f6c19">d5618e5a</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-20T10:57:50+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/rules: set LC_ALL to fix groff warnings in the manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/0f6f9b964b1ff89a8ad1753ece14d0893a2148e5">0f6f9b96</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-20T11:05:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/patches/spelling: fix some typos
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/4e3c9da2c6adca5ff0b13c237c94d080f0d6495d">4e3c9da2</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-20T11:23:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">strip erroneous rpath
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/adb38f3c01f25c77a23db51c8f2ec0df0fcfcb5a">adb38f3c</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-20T11:25:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debian/rules: improve the clean target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/736cca45fe755b0db26c386d0d8d6a00b5ca3b62">736cca45</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-20T11:32:43+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">silence lintian false-positive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/-/commit/9e1fadefc4b130ecff00222b42b7a10d02dafea7">9e1fadef</a></strong>
<div>
<span>by Michael R. Crusoe</span>
<i>at 2021-02-20T11:34:39+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload lintian clean package
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#e30387ef4558622af8ca77d2ea7e92d87fcc2331">
<span class="new-file">
+
debian/hyphy-common.lintian-overrides
</span>
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</li>
<li class="file-stats">
<a href="#736c6bc0ca2ba9855b5819bfc4a7797bc0701807">
<span class="new-file">
+
debian/hyphy-mpi.lintian-overrides
</span>
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<li class="file-stats">
<a href="#f829438d138d5ed9c9570e7ec0589b81d1485bb8">
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+
debian/hyphy-pt.lintian-overrides
</span>
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<li class="file-stats">
<a href="#c72fadc42d1caaada4fa7786d43a551db6e91b8b">
debian/manuals/hyphy.1
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
<li class="file-stats">
<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">
<span class="new-file">
+
debian/patches/spelling
</span>
</a>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy (2.5.28+dfsg-2) unstable; 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"> * Team upload.</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"> * debian/rules: set LC_ALL to fix groff warnings in the manpages</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"> * debian/patches/spelling: fix some typos</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"> * debian/rules: delete erroneous rpath for the MPI binaries</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"> * debian/rules: improve the clean target</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"> -- Michael R. Crusoe <crusoe@debian.org> Sat, 20 Feb 2021 10:57:19 +0100</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">hyphy (2.5.28+dfsg-1) unstable; urgency=medium</span>
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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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload.</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,8 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libcurl4-gnutls-dev | libcurl4-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libssl-dev,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libsqlite3-dev,</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> pkg-config</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> pkg-config,</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> chrpath</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Standards-Version: 4.5.1</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/hyphy</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/hyphy.git</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#e30387ef4558622af8ca77d2ea7e92d87fcc2331"><strong>debian/hyphy-common.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy-common: package-contains-documentation-outside-usr-share-doc usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md</span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#736c6bc0ca2ba9855b5819bfc4a7797bc0701807"><strong>debian/hyphy-mpi.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy-mpi: typo-in-manual-page usr/share/man/man1/HYPHYMPI.1.gz gard guard</span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#f829438d138d5ed9c9570e7ec0589b81d1485bb8"><strong>debian/hyphy-pt.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">hyphy-pt: typo-in-manual-page usr/share/man/man1/hyphy.1.gz gard guard</span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#c72fadc42d1caaada4fa7786d43a551db6e91b8b"><strong>debian/manuals/hyphy.1</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -217,7 +217,7 @@ prr</td>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="plaintext">Using the model and the outgroup provided by the user, perform relative rate tests with all possible pair of species from the data file.</span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext">prrti</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext">Given a list of files (and optinally genetic code tables), perform relative ratio tests on all possible pair of the data files.</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">Given a list of files (and opti<span class="idiff left right">o</span>nally genetic code tables), perform relative ratio tests on all possible pair of the data files.</span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext">pdf</span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext">Read sequence data, select a contiguous subset of sites and save it to another datafile.</span>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_sqlite.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">rm_arch_specific_flags.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">spelling</span></pre>
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<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <crusoe@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: fix typos</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/veg/hyphy/pull/1289</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hyphy.orig/src/core/category.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hyphy/src/core/category.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">@@ -177,7 +177,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> !CheckEqual (iSplitter->GetMaxX(),1.0) ||</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> *theName == splitterName ||</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> (intervals = iSplitter->GetNumberOfIntervals()+1) < 2) {</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- HandleApplicationError (errorMsg & _String("Category variables which specify interval splitting options must be supported on [0,1], and not result in circular dependance"));</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ HandleApplicationError (errorMsg & _String("Category variables which specify interval splitting options must be supported on [0,1], and not result in circular dependence"));</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> return;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -475,7 +475,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // disallow category -> category dependance</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // disallow category -> category dependence</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> for (long i=0; i<scannedVarsList.lLength; i++) {</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> _Variable * curVar = (_Variable*)variablePtrs (scannedVarsList.list_data[i]);</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> if (curVar->IsCategory()) {</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -489,7 +489,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> hiddenMarkovModel = HY_NO_MODEL;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> parameterList.Duplicate (&scannedVarsList);</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // finally go thru all the variables and put them where they belong in dependance containers</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // finally go thru all the variables and put them where they belong in dependence containers</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> _SimpleList exclude;</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hyphy.orig/res/TemplateBatchFiles/files.lst</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hyphy/res/TemplateBatchFiles/files.lst</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -108,4 +108,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> "","Perform relative ratio tests.","!Relative Ratio";</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> "RRT","Use relative ratio test on 2 datasets and a variety of standard models","RelativeRatio.bf";</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-"PRRTI","Given a list of files (and optinally genetic code tables), perform relative ratio tests on all possible pair of the data files.","PairwiseRelativeRatio.bf";</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+"PRRTI","Given a list of files (and optionally genetic code tables), perform relative ratio tests on all possible pair of the data files.","PairwiseRelativeRatio.bf";</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- hyphy.orig/src/core/likefunc.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ hyphy/src/core/likefunc.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="p">@@ -2382,20 +2382,20 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> //_______________________________________________________________________________________</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-void _LikelihoodFunction::RecurseConstantOnPartition (long blockIndex, long index, long dependance, long highestIndex, hyFloat weight, _Matrix& cache) {</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+void _LikelihoodFunction::RecurseConstantOnPartition (long blockIndex, long index, long dependence, long highestIndex, hyFloat weight, _Matrix& cache) {</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> // SLKP 20210102: TODO this needs to be reviewed and confirmed as working.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> _CategoryVariable* thisC = (_CategoryVariable*)LocateVar(indexCat.list_data[index]);</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> if (index<highestIndex) {</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ((!CheckNthBit(dependance,index))||thisC->is_hidden_markov()) {</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RecurseCategory (blockIndex, index+1, dependance,highestIndex,weight);</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if ((!CheckNthBit(dependence,index))||thisC->is_hidden_markov()) {</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RecurseCategory (blockIndex, index+1, dependence,highestIndex,weight);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> } else {</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> thisC->Refresh();</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> long nI = thisC->GetNumberOfIntervals ();</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> offsetCounter *= nI;</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> for (long k = 0; k<nI; k++) {</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> thisC->SetIntervalValue(k);</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RecurseConstantOnPartition(blockIndex,index+1,dependance, highestIndex,weight*thisC->GetIntervalWeight(k),cache);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RecurseConstantOnPartition(blockIndex,index+1,dependence, highestIndex,weight*thisC->GetIntervalWeight(k),cache);</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> categID+=offsetCounter/nI;</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> }</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> offsetCounter/=nI;</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -2450,7 +2450,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> //_______________________________________________________________________________________</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-void _LikelihoodFunction::RecurseCategory(long blockIndex, long index, long dependance, long highestIndex, hyFloat weight</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+void _LikelihoodFunction::RecurseCategory(long blockIndex, long index, long dependence, long highestIndex, hyFloat weight</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> #ifdef _SLKP_LFENGINE_REWRITE_</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> ,_SimpleList* siteMultipliers, char runMode, hyFloat *runStorage,</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> long branchIndex, _SimpleList* branchValues</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="p">@@ -2459,8 +2459,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> {</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> _CategoryVariable* thisC = (_CategoryVariable*)LocateVar(indexCat.list_data[index]);</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> if (index<highestIndex) {</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if ((!CheckNthBit(dependance,index))||thisC->is_hidden_markov())</span></span>
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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;">- RecurseCategory (blockIndex, index+1, dependance,highestIndex,weight</span></span>
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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 ((!CheckNthBit(dependence,index))||thisC->is_hidden_markov())</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RecurseCategory (blockIndex, index+1, dependence,highestIndex,weight</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> #ifdef _SLKP_LFENGINE_REWRITE_</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> ,siteMultipliers,runMode,runStorage</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> #endif</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="p">@@ -2471,7 +2471,7 @@</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> offsetCounter *= nI;</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> for (long k = 0; k<nI; k++) {</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> thisC->SetIntervalValue(k);</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- RecurseCategory(blockIndex,index+1,dependance, highestIndex,weight*thisC->GetIntervalWeight(k)</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ RecurseCategory(blockIndex,index+1,dependence, highestIndex,weight*thisC->GetIntervalWeight(k)</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> #ifdef _SLKP_LFENGINE_REWRITE_</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> ,siteMultipliers,runMode,runStorage,branchIndex,branchValues</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> #endif</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="p">@@ -2698,7 +2698,7 @@</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> {</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> _Matrix dependancies (MAX(3,indexDep.lLength),indexInd.lLength,true,true);</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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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;">- // element (i,j) represents the dependance of i-th dep var on the j-th ind var</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // element (i,j) represents the dependence of i-th dep var on the j-th ind var</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> // 0 - no dep,</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> // 1 -> monotone increase,</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> // -1 -> monotone decrease</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="p">@@ -7678,7 +7678,7 @@</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> avl.ReorderList();</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> </span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (templateKind<0) { // remove dependance of the function from the HMM model specifier</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (templateKind<0) { // remove dependence of the function from the HMM model specifier</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> allVariables.Delete (allVariables.Find(-templateKind-1));</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> rankVariables.Delete ((BaseRef)(-templateKind-1));</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> }</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,6 +3,7 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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7
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,6 +16,10 @@ ISOFILES += res/TemplateBatchFiles/TemplateModels/models.lst</td>
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15
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> dh $@ --buildsystem=cmake</span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> dh_auto_clean --builddirectory obj-avx</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh_auto_clean --builddirectory obj-sse3</span>
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<td class="diff-line-num new old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="43" style="width: 35px; color: rgba(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="48" style="width: 35px; color: rgba(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">@@ -43,6 +48,7 @@ endif</td>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(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="LC49" class="line" lang="plaintext">override_dh_install-arch:</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext"> dh_install -a</span>
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<td class="diff-line-num new old_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">
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> chrpath --delete obj-*/HYPHYMPI</span>
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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(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="LC52" class="line" lang="plaintext">ifeq (amd64,$(DEB_HOST_ARCH))</span>
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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> mkdir -p debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin</span>
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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(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="LC54" class="line" lang="plaintext"> mkdir -p debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin</span>
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