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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/roguenarok">Debian Med / roguenarok</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6">db6f4ec9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-07T10:23:41+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.1</pre>
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<h4>18 changed files:</h4>
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
README
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<li class="file-stats">
<a href="#ecc29ad49317b48958d32a742dffaee9e25811f5">
RogueNaRok.c
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<li class="file-stats">
<a href="#a9656aa44b0c4ef013e784e30a79e13b810f2bc1">
Tree.c
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<li class="file-stats">
<a href="#668e20ebd05f7b0a5d1c08ae01a24fb0d6c92e5a">
Tree.h
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<li class="file-stats">
<a href="#e25f9d52b876786bfa1c7fd2b1f1e9ce63820bf0">
common.c
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<li class="file-stats">
<a href="#5650fde78be1a4aa63187b0ead35921d9cadc490">
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+
example/150.bs
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<li class="file-stats">
<a href="#8f12b26b66be08c8357fa1a17dffccf7d74c6f1e">
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example/150.tre
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<li class="file-stats">
<a href="#52a13c344719faea5b743411f4e561db3edf7391">
legacy.h
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<li class="file-stats">
<a href="#9af880e6dd007e5135b414c8f65fb71705c580f7">
newFunctions.c
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<li class="file-stats">
<a href="#63e54bce530c748026cee12754492dc2952a5fb5">
newFunctions.h
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<li class="file-stats">
<a href="#debddb03489670d1c5b62a83303cb1918c5bbd9b">
parallel.c
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<li class="file-stats">
<a href="#6d33ee8f573cb1d3907a0c062b739f860d57d16b">
rnr-lsi.c
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<li class="file-stats">
<a href="#564056cc21f0e2f9f97b1e698e25cf7a4bd3915b">
rnr-mast.c
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<li class="file-stats">
<a href="#31bc0c7d7009021cf0b86050fdf205abf3c73a28">
rnr-prune.c
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<li class="file-stats">
<a href="#13fe96832b46c053d9d1db4e3e3597afc55357ae">
rnr-tii.c
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<li class="file-stats">
<a href="#cd02ee1411f35dbba48aee4f1ac519a4be3e131f">
sharedVariables.h
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<li class="file-stats">
<a href="#69e22c5499a98ab6a75ce802eb8a292d35297398">
<span class="new-file">
+
utils/pruneWrapper.sh
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<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">CC</span> <span class="o" style="font-weight: 600;">=</span> gcc </span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-D_GNU_SOURCE</span><span class="idiff left"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right"># -DNDEBUG</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-Wall</span> <span class="nt" style="color: #000080;">-D_GNU_SOURCE</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">LFLAGS</span> <span class="o" style="font-weight: 600;">=</span> <span class="nt" style="color: #000080;">-lm</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(mode), debug)</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"> <span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-g</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"> <span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="c" style="color: #998; font-style: italic;"># -march=native</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"> <span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;"><span class="idiff left">-DNDEBUG</span></span><span class="idiff right"> </span><span class="c" style="color: #998; font-style: italic;"># -march=native</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(mode), profile)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"> <span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-pg</span> <span class="nt" style="color: #000080;">-g</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" 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="33" 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">@@ -33,20 +33,20 @@ mast-objs = rnr-mast.o common.o List.o Tree.o BitVector.o HashTable.o legacy.o n</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="make"><span class="nv" style="color: #008080;">prune-objs</span> <span class="o" style="font-weight: 600;">=</span> rnr-prune.o common.o Tree.o BitVector.o HashTable.o legacy.o newFunctions.o List.o</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"><span class="nl">rnr-lsi</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(lsi-objs)</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">L</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="idiff"> </span><span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff right">C</span>FLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">C</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff">L</span>FLAGS)</span><span class="idiff right"> </span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="make"><span class="nl">rnr-tii</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(tii-objs)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">L</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="idiff"> </span><span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff right">C</span>FLAGS)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">C</span>FLAGS)</span> <span class="idiff"> </span><span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff">L</span>FLAGS)</span><span class="idiff right"> </span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"><span class="nl">rnr-mast</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(mast-objs)</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">L</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="idiff"> </span><span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff right">C</span>FLAGS)</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">C</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff">L</span>FLAGS)</span><span class="idiff right"> </span></span>
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41
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="make"><span class="nl">rnr-prune</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(prune-objs)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">L</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="idiff"> </span><span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff right">C</span>FLAGS)</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">C</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff">L</span>FLAGS)</span><span class="idiff right"> </span></span>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"><span class="k" style="font-weight: 600;">ifeq</span> <span class="nv" style="color: #008080;">($(mode),parallel)</span></span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="make"><span class="nl">RogueNaRok</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(rnr-objs)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">L</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span><span class="nt" style="color: #000080;">-parallel</span> <span class="idiff"> </span><span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff right">C</span>FLAGS)</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">C</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span><span class="nt" style="color: #000080;">-parallel</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff">L</span>FLAGS)</span><span class="idiff right"> </span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="make"><span class="k" style="font-weight: 600;">else</span></span>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="make"><span class="nl">RogueNaRok</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(rnr-objs)</span></span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">L</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="idiff"> </span><span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff right">C</span>FLAGS)</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(<span class="idiff left">C</span>FLAGS)</span> <span class="nt" style="color: #000080;">-o</span> <span class="nv" style="color: #008080;">$@</span> <span class="nv" style="color: #008080;">$^</span> <span class="nv" style="color: #008080;">$(<span class="idiff">L</span>FLAGS)</span><span class="idiff right"> </span></span>
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="make"><span class="k" style="font-weight: 600;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="make"><span class="nl">%.o </span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">%.c $(DEPS)</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#69e27356ef629022720d868ab0c0e3394775b6c1"><strong>README</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,4 +11,22 @@ trigger the help message. Just follow the instructions.</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">More info is available on</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">https://github.com/aberer/RogueNaRok/wiki/RogueNaRok . Also, use this</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">site for reporting bugs, ask questions of how to employ RogueNaRok.</span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">site for reporting bugs or ask questions of how to employ RogueNaRok.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">QUICK START: </span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Have a look in the "example"-directory. For calling RogueNaRok, simply execute </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">./RogueNaRok -i example/150.bs -n id</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">in the command line. </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Searching for rogues based on bootstrap values drawn onto a ML tree</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">(from a bootstrap tree set) is done with</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ./RogueNaRok -i example/150.bs -t example/150.tre -n id</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">Also notice the script utils/pruneWrapper.sh. It facilitates the</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">process of obtaining pruned trees from the RogueNaRok search. Call</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">without arguments and follow the instructions in the help message.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">CITATION: </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">If RogueNaRok has been useful for your work, please cite as: </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">* A.J. Aberer, D. Krompass, A. Stamatakis: "Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice", Systematic Biology, in press.</span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#ecc29ad49317b48958d32a742dffaee9e25811f5"><strong>RogueNaRok.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1079,7 +1079,9 @@ void printRogueInformationToFile( All *tr, FILE *rogueOutput, int bestCumEver, i</td>
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="c"> <span class="n" style="color: #333;">printIndexListToFile</span><span class="p">(</span><span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="n" style="color: #333;">dropsetInRound</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">taxaToDrop</span><span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1081" class="line" lang="c"> <span class="n" style="color: #333;">fprintRogueNames</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="n" style="color: #333;">dropsetInRound</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">taxaToDrop</span><span class="p">);</span></span>
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1082
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<pre style="margin: 0;">-<span id="LC1082" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">cumScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cumScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">)</span><span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numberOfTrees</span><span class="p">,(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">cumScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)((</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">mxtips</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">);</span> </span>
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">cumScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cumScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="p">)</span><span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="c"> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">cumScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)((</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">mxtips</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="c"> <span class="n" style="color: #333;">reached</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bestCumEver</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cumScores</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="c"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="c"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1570,10 +1572,10 @@ Dropset *evaluateEvents(HashTable *mergingHash, Array *bipartitionsById, Array *</td>
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<pre style="margin: 0;"> <span id="LC1572" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC1573" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">oldQuality</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">labelPenalty</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> </span>
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<pre style="margin: 0;"> <span id="LC1574" class="line" lang="c"> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improvement</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">drSize</span> </span>
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<pre style="margin: 0;">-<span id="LC1573" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improvement</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">resSize</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1575" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improvement</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;"><span class="idiff left">labelPenalty</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">resSize</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1576" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">newQuality</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">labelPenalty</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> </span>
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1577
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<pre style="margin: 0;"> <span id="LC1577" class="line" lang="c"> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">dropset</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improvement</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">resSize</span></span>
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<pre style="margin: 0;">-<span id="LC1576" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">dropset</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improvement</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">drSize</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC1578" class="line" lang="c"> <span class="o" style="font-weight: 600;">:</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">dropset</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improvement</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">))</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;"><span class="idiff left">labelPenalty</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff right"> </span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">drSize</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC1579" class="line" lang="c"> </span>
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1580
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<pre style="margin: 0;"> <span id="LC1580" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">newQuality</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">oldQuality</span><span class="p">)</span> <span class="p">)</span></span>
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1581
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<pre style="margin: 0;"> <span id="LC1581" class="line" lang="c"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dropset</span><span class="p">;</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1584" 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">@@ -1584,11 +1586,15 @@ Dropset *evaluateEvents(HashTable *mergingHash, Array *bipartitionsById, Array *</td>
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1584
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1586
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<pre style="margin: 0;"> <span id="LC1586" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">allDropsets</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">arrayTable</span><span class="p">);</span></span>
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1587
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<pre style="margin: 0;"> <span id="LC1587" class="line" lang="c"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">allDropsets</span><span class="p">);</span></span>
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1588
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<pre style="margin: 0;"> <span id="LC1588" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC1587" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">labelPenalty</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">improvement</span></span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1589" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(<span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">improvement</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">computeSupport</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">numberOfTrees</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">labelPenalty</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">lengthIndexList</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">result</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">taxaToDrop</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="idiff right"> </span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC1590" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1589" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">labelPenalty</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">improvement</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span><span class="p">.</span><span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">lengthIndexList</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">taxaToDrop</span><span class="p">))</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">.</span><span class="mi" style="color: #099;">0</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1590" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span> </span>
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1591
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<pre style="margin: 0;">-<span id="LC1591" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span> </span>
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1591
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<pre style="margin: 0;">+<span id="LC1591" class="line" lang="c"></span>
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1592
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<pre style="margin: 0;">+<span id="LC1592" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* if(labelPenalty == 0.0 && result->improvement > 0) */</span></span>
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1593
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* return result; */</span></span>
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<pre style="margin: 0;">+<span id="LC1594" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* else if(labelPenalty != 0.0 && (result->improvement / (computeSupport ? numberOfTrees : 1.0) - labelPenalty * lengthIndexList(result->taxaToDrop)) > 0.0 ) */</span></span>
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1595
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<pre style="margin: 0;">+<span id="LC1595" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* return result; */</span></span>
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<pre style="margin: 0;">+<span id="LC1596" class="line" lang="c"></span>
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1597
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<pre style="margin: 0;">+<span id="LC1597" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC1598" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1599" class="line" lang="c"><span class="p">}</span></span>
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1600
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<pre style="margin: 0;"> <span id="LC1600" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1917,8 +1923,7 @@ void doomRogues(All *tr, char *bootStrapFileName, char *dontDropFile, char *tree</td>
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<pre style="margin: 0;"> <span id="LC1923" class="line" lang="c"></span>
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1918
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1924
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<pre style="margin: 0;"> <span id="LC1924" class="line" lang="c"> <span class="n" style="color: #333;">bestLastTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cumScore</span><span class="p">;</span></span>
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1919
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1925
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<pre style="margin: 0;"> <span id="LC1925" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="s" style="color: #d14;">"num</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">taxNum</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">taxon</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">rawImprovement</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">RBIC</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1920
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<td class="new_line diff-line-num old" data-linenumber="1926" 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="LC1920" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">cumScore</span> <span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">mxtips</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">);</span></span>
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1921
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<pre style="margin: 0;">-<span id="LC1921" class="line" lang="c"></span>
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1926
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<pre style="margin: 0;">+<span id="LC1926" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">rogueOutput</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%d</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">%f</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">cumScore</span> <span class="o" style="font-weight: 600;">/</span><span class="p">(</span> <span class="p">(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">mxtips</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">))</span> <span class="p">);</span> </span>
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1927
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<pre style="margin: 0;"> <span id="LC1927" class="line" lang="c"> <span class="n" style="color: #333;">PR</span><span class="p">(</span><span class="s" style="color: #d14;">"[%f] initialisation done (initScore = %f, numBip=%d)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">updateTime</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">timeInc</span><span class="p">),</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">cumScore</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)((</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">computeSupport</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numberOfTrees</span> <span class="o" style="font-weight: 600;">:</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span> <span class="p">),</span> <span class="n" style="color: #333;">bipartitionsById</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>
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1923
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1928
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<pre style="margin: 0;"> <span id="LC1928" class="line" lang="c"></span>
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1929
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<pre style="margin: 0;"> <span id="LC1929" class="line" lang="c"> <span class="n" style="color: #333;">boolean</span> <span class="n" style="color: #333;">firstMerge</span><span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TRUE</span><span class="p">;</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2162,7 +2167,7 @@ int main(int argc, char *argv[])</td>
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2162
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2167
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<pre style="margin: 0;"> <span id="LC2167" class="line" lang="c"> <span class="n" style="color: #333;">programVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PROG_VERSION</span><span class="p">;</span></span>
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2163
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2168
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<pre style="margin: 0;"> <span id="LC2168" class="line" lang="c"> <span class="n" style="color: #333;">programReleaseDate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PROG_RELEASE_DATE</span><span class="p">;</span></span>
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2169
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<pre style="margin: 0;"> <span id="LC2169" class="line" lang="c"> </span>
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2165
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<pre style="margin: 0;">-<span id="LC2165" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"i:t:n:x:whc:s:bT:L:"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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2170
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<pre style="margin: 0;">+<span id="LC2170" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span> <span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"i:t:n:x:w<span class="idiff left right">:</span>hc:s:bT:L:"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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2171
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<pre style="margin: 0;"> <span id="LC2171" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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2172
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<pre style="margin: 0;"> <span id="LC2172" class="line" lang="c"> <span class="p">{</span></span>
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2168
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<pre style="margin: 0;"> <span id="LC2173" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'i'</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#a9656aa44b0c4ef013e784e30a79e13b810f2bc1"><strong>Tree.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -326,6 +326,21 @@ nodeptr findAnyTip(nodeptr p, int numsp)</td>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="c"><span class="p">}</span> </span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hookupAdd</span><span class="p">(</span><span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numBranches</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="p">;</span> </span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="c"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="c"></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">numBranches</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="c"> <span class="p">{</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="c"> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> </span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="c"> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">z</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span> </span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="c"> <span class="p">}</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="c"><span class="p">}</span></span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="c"></span>
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hookup</span> <span class="p">(</span><span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">z</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numBranches</span><span class="p">)</span></span>
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="c"><span class="p">{</span></span>
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="944" 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="959" 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">@@ -944,7 +959,7 @@ static boolean treeNeedCh (FILE *fp, int c1, char *where)</td>
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944
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959
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<pre style="margin: 0;"> <span id="LC959" class="line" lang="c"> <span class="n" style="color: #333;">putchar</span><span class="p">(</span><span class="sc" style="color: #d14;">'\n'</span><span class="p">);</span></span>
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945
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960
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<pre style="margin: 0;"> <span id="LC960" class="line" lang="c"></span>
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946
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">c1</span> <span class="o" style="font-weight: 600;">==</span> <span class="sc" style="color: #d14;">':'</span><span class="p">)</span> </span>
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947
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<pre style="margin: 0;">-<span id="LC947" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"R<span class="idiff left right">AxML</span> may be expecting to read a tree that contains branch lengths</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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962
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<pre style="margin: 0;">+<span id="LC962" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"R<span class="idiff left right">ogueNaRok</span> may be expecting to read a tree that contains branch lengths</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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948
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="c"></span>
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949
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964
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>
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950
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965
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<pre style="margin: 0;"> <span id="LC965" class="line" lang="c"><span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1163,8 +1178,8 @@ int treeReadLen (FILE *fp, All *tr,</td>
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1163
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1178
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<pre style="margin: 0;"> <span id="LC1178" class="line" lang="c"> <span class="p">{</span></span>
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1164
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">completeTree</span><span class="p">)</span></span>
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1165
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="c"> <span class="p">{</span></span>
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1166
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<pre style="margin: 0;">-<span id="LC1166" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"Hello this is your friendly R<span class="idiff left right">AxML</span> tree parsing routine</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1167
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<pre style="margin: 0;">-<span id="LC1167" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"The R<span class="idiff left right">AxML</span> option you are uisng requires to read in only complete trees</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1181
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<pre style="margin: 0;">+<span id="LC1181" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"Hello this is your friendly R<span class="idiff left right">ogueNaRok</span> tree parsing routine</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1182
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<pre style="margin: 0;">+<span id="LC1182" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"The R<span class="idiff left right">ogueNaRok</span> option you are uisng requires to read in only complete trees</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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1168
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1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"with %d taxa, there is at least one tree with %d taxa though ... exiting</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">ntips</span><span class="p">);</span></span>
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1169
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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1170
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#668e20ebd05f7b0a5d1c08ae01a24fb0d6c92e5a"><strong>Tree.h</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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">@@ -49,6 +49,7 @@ boolean setupTree (All *tr, char *bootstrapTrees);</td>
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">readBestTree</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">readBootstrapTree</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">file</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hookupDefault</span> <span class="p">(</span><span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numBranches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">hookupAdd</span> <span class="p">(</span><span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numBranches</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="n" style="color: #333;">nodeptr</span> <span class="nf" style="color: #900; font-weight: 600;">findAnyTip</span><span class="p">(</span><span class="n" style="color: #333;">nodeptr</span> <span class="n" style="color: #333;">p</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numsp</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">treeFindTipByLabelString</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">str</span><span class="p">,</span> <span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">getTreeStringLength</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fileName</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "common.h"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ALLOW_OVERWRITE_INFO_FILE <span class="idiff left right">TRU</span>E</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define ALLOW_OVERWRITE_INFO_FILE <span class="idiff left right">FALS</span>E</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">printHelpFile</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" 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">@@ -129,7 +129,7 @@ FILE *myfopen(const char *path, const char *mode)</td>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="c"> <span class="p">{</span></span>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">processID</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"The file %s R<span class="idiff left right">AxML</span> wants to open for writing or appending can not be opened [mode: %s], exiting ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"The file %s R<span class="idiff left right">ogueNaRok</span> wants to open for writing or appending can not be opened [mode: %s], exiting ...</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span></span>
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" 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="142" 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">@@ -142,6 +142,13 @@ void setupInfoFile()</td>
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142
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="p">{</span></span>
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CALLOC</span><span class="p">(</span><span class="mi" style="color: #099;">1024</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">workdir</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">workdir</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">))</span> </span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="c"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* TODO not windows compatible */</span> </span>
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<td class="new_line diff-line-num new" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">"/"</span><span class="p">);</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="c"> <span class="p">}</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="c"></span>
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145
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">programName</span><span class="p">);</span></span>
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146
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">"_info"</span><span class="p">);</span></span>
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147
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">"."</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="156" 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">@@ -149,7 +156,7 @@ void setupInfoFile()</td>
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149
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="c"> </span>
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150
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">NOT</span> <span class="n" style="color: #333;">ALLOW_OVERWRITE_INFO_FILE</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">filexists</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">))</span></span>
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151
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="c"> <span class="p">{</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"The run-id >%s< you specified already exists. Aborting in order to protect the output of this previous run.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">run_id</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="c"> <span class="n" style="color: #333;">printf</span><span class="p">(</span><span class="s" style="color: #d14;">"The run-id >%s< you specified already exists<span class="idiff left"> in folder >%s<</span>. Aborting in order to protect the output of this previous run.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">run_id</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">workdir</span></span><span class="p">);</span></span>
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153
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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154
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="c"> <span class="p">}</span></span>
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155
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="c"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" 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="189" 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">@@ -182,6 +189,12 @@ FILE *getOutputFileFromString(char *fileName)</td>
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182
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="c"></span>
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183
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="mi" style="color: #099;">1024</span><span class="p">];</span></span>
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184
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">workdir</span><span class="p">);</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="c"></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">workdir</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">))</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="c"> <span class="p">{</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">"/"</span><span class="p">)</span> <span class="p">;</span> </span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="c"> <span class="p">}</span> </span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="c"></span>
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185
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">programName</span><span class="p">);</span></span>
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186
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">"_"</span><span class="p">);</span></span>
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187
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="c"> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">fileName</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#5650fde78be1a4aa63187b0ead35921d9cadc490"><strong>example/150.bs</strong></a>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#8f12b26b66be08c8357fa1a17dffccf7d74c6f1e"><strong>example/150.tre</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">(Species223:0.10167067874101318181,((((((Species003:0.02885845688515585247,Species081:0.02366007644437243332):0.01294473315506602072,(Species086:0.02889623396833742794,((Species180:0.01130259274235604489,Species082:0.00588430659940250220):0.00981390388086450342,(Species065:0.00646683874069644074,Species004:0.01539670034795830554):0.01619225310325838815):0.00429514506342924384):0.01971746273545336645):0.00831177461738581355,((Species125:0.05085075934513810098,((Species014:0.49797318153312469802,((((Species011:1.23308538517097043830,(Species194:0.14277715768862139778,((Species161:0.07693527997946790487,Species226:0.08279880317510759924):0.03473670874692073168,(Species101:0.18362307169916605720,Species084:0.04516914418689594451):0.02600460300574566549):0.16302716763912183939):0.17152603152321063695):0.29181069263101583333,(((Species067:0.07436559248911303599,(Species066:0.16358806787391069748,Species188:0.06727442521066734349):0.03143305333089802672):0.42058509774974650597,((Species139:0.02755893932934918786,Species138:0.00927623378224346797):0.31291243044378824756,(Species135:0.05355187624018638293,(Species225:0.04095925546627367242,Species136:0.04529428377253751775):0.02264909429426772633):0.10853612397239845166):0.66486369152103907965):0.30397382688577473386,((Species229:0.11967685776574145395,Species072:0.11440477386882896838):0.33916096231786774240,(Species064:0.20266166198809190679,Species071:0.14493450751437683688):0.21858983245942087414):0.25666638095603350189):0.27358515136283018121):0.07415813760549078149,(Species227:0.25061592278519256860,Species228:0.33552464317357100221):0.52574389080471883862):0.10756188842616883072,((((Species012:0.01417722547707581278,Species010:0.04034675130093703932):0.16904419090996167241,(Species061:0.09506350436512521485,Species013:0.12421437508335884947):0.06353262550134237963):0.07673489121367255139,Species050:0.41201708114686891316):0.27147070082890234488,Species142:0.41539748717590579963):0.50972915079833658325):0.09759638563324000982):0.99230472005323211437,Species201:0.07266950601481036998):0.08368818168222916243):0.08661336847999560884,Species126:0.02856780795792028538):0.02727351043682214177):0.00554677692418998128,((Species070:0.03640110525322296647,(((((((Species056:0.05810146368000065897,(Species193:0.15527480906281457274,Species103:0.02587352836178205551):0.02205993706280176200):0.08626560337949243373,(Species192:0.08228987525224805422,Species195:0.01857892203414495888):0.01470797268224145402):0.01543578392835846802,(Species078:0.04106610111964105470,Species190:0.02903751298979457759):0.05771760873020609361):0.04702978953187943179,((Species043:0.09507147866835705119,(Species046:0.02035057958620751714,((Species069:0.01518990555238271777,Species063:0.02517606796483481957):0.04662020858163388320,(Species232:0.00591839728771769401,Species144:0.02170953083404570522):0.04424175790032577188):0.02982797999134110048):0.04395678894111249013):0.03621104380457264293,(Species008:0.01814609097843261631,Species023:0.04200898296839167961):0.08106701587147051302):0.00441465903382823929):0.01373025854248415348,(Species022:0.02672670461500788186,(((Species191:0.01619226906191993318,(Species034:0.03901491474236817858,Species038:0.09306202168426473686):0.02646811159994764615):0.00694110928044117895,(Species105:0.03628664324670868163,Species137:0.05602046049874488676):0.00798710843626010934):0.00512799958104748991,Species132:0.02743939045371524693):0.00560621124187029966):0.00535275732403040026):0.00145271493784958653,Species175:0.15438504415258511027):0.00458822419427611095,Species122:0.02798633843870117557):0.00780564792301203635):0.00312224678707470659,(Species120:0.05902402956750785884,(((Species073:0.02708812772465343799,Species114:0.06035918102667164886):0.02335100292363243360,(Species173:0.08473561568135122568,(Species099:0.10639514904357490199,(Species117:0.08649659485712282714,Species181:0.04475646988096785434):0.01574305223840075443):0.00715281952797727251):0.00965263800183392348):0.02942778338316406547,((Species196:0.16305716817873328051,(Species179:0.08295252148450747709,Species119:0.03445856197247401664):0.02103572893837889202):0.01020118422265344459,(Species058:0.01649265380172335732,Species005:0.03540157947407617661):0.02730045183405632042):0.02685130245022435830):0.01955698773156188883):0.01401521366387832417):0.00645864506977414984):0.01452668071274556584,((Species202:0.02560241781269579839,Species164:0.03436623016886058285):0.00611998201561592039,((Species060:0.00823394383196080631,(((((Species090:0.02288034169619141203,(Species177:0.00380275336783937514,Species104:0.00891618894771329523):0.00451130671569329334):0.00592183447845993395,(Species054:0.02249379127832184036,Species159:0.00938914355909220219):0.00413880610036351359):0.00340936612896344717,(Species231:0.08782358907112357282,Species155:0.15110968039987382472):0.01816672189179855887):0.00619962611770736444,(Species027:0.01017648464661234306,(Species040:0.02419170078610901817,Species160:0.01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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#52a13c344719faea5b743411f4e561db3edf7391"><strong>legacy.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,6 +138,6 @@ ProfileElem *addProfileElem(entry *helem, int vectorLength, int treeVectorLength</td>
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"><span class="n" style="color: #333;">BitVector</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">neglectThoseTaxa</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">toDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">considerBranchLengths</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="c"><span class="n" style="color: #333;">BitVector</span> <span class="o" style="font-weight: 600;">**</span><span class="nf" style="color: #900; font-weight: 600;">initBitVector</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">BitVector</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vectorLength</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#9af880e6dd007e5135b414c8f65fb71705c580f7"><strong>newFunctions.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,7 +49,7 @@ IndexList *parseToDrop(All *tr, FILE *toDrop)</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">considerBranchLengths</span></span><span class="p">)</span> </span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">k</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)(</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">)));</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,8 +58,11 @@ void pruneTaxon(All *tr, unsigned int k)</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">back</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">q1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">back</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">q2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">next</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">back</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="c"> <span class="n" style="color: #333;">hookupDefault</span><span class="p">(</span><span class="n" style="color: #333;">q1</span><span class="p">,</span> <span class="n" style="color: #333;">q2</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numBranches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">considerBranchLengths</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">hookupAdd</span><span class="p">(</span><span class="n" style="color: #333;">q1</span><span class="p">,</span><span class="n" style="color: #333;">q2</span><span class="p">,</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numBranches</span><span class="p">);</span> </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">hookupDefault</span><span class="p">(</span><span class="n" style="color: #333;">q1</span><span class="p">,</span><span class="n" style="color: #333;">q2</span><span class="p">,</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">numBranches</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">findAnyTip</span><span class="p">(</span><span class="n" style="color: #333;">q1</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> </span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#63e54bce530c748026cee12754492dc2952a5fb5"><strong>newFunctions.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -38,7 +38,7 @@</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "ProfileElem.h"</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="n" style="color: #333;">IndexList</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">parseToDrop</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">toDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p"><span class="idiff left right">)</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">k</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">boolean</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">considerBranchLengths</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> </span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"><span class="n" style="color: #333;">BitVector</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">neglectThoseTaxa</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">toDrop</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="n" style="color: #333;">Array</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">getOriginalBipArray</span><span class="p">(</span><span class="n" style="color: #333;">All</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bestTree</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">FILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">treeFile</span><span class="p">)</span> <span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#debddb03489670d1c5b62a83303cb1918c5bbd9b"><strong>parallel.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,7 +54,7 @@ void pinToCore(int tid)</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">pthread_setaffinity_np</span><span class="p">(</span><span class="n" style="color: #333;">pthread_self</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">cpu_set_t</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cpuset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">There was a problem finding a physical core for thread number %d to run on.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">tid</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"Probably this happend because you are trying to run more threads than you have cores available,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"Probably this happen<span class="idiff left right">e</span>d because you are trying to run more threads than you have cores available,</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"which is a thing you should never ever do again, good bye .... </span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="p">}</span></span>
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<li id="6d33ee8f573cb1d3907a0c062b739f860d57d16b">
<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#6d33ee8f573cb1d3907a0c062b739f860d57d16b"><strong>rnr-lsi.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,8 +47,8 @@</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_NAME "RnR-lsi"</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_VERSION "1.0"</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_RELEASE_DATE "20<span class="idiff left">1</span>1-<span class="idiff right">10-25</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_VERSION "1.0<span class="idiff left right">.1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PROG_RELEASE_DATE "20<span class="idiff left">2</span>1-<span class="idiff right">06-07</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define FLIP_NTH_BIT(bitVector,n) (bitVector[(n) / MASK_LENGTH] |= mask32[ (n) % MASK_LENGTH ])</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define NTH_BIT_IS_SET(bitVector,n) (bitVector[(n) / MASK_LENGTH] & mask32[(n) % MASK_LENGTH])</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -244,7 +244,7 @@ void calculateLeafStability(All *tr, char *bootstrapFileName, char *excludeFileN</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> <span class="n" style="color: #333;">readBootstrapTree</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">bootstrapFile</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">FOR_0_LIMIT</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">,</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">NOT</span> <span class="n" style="color: #333;">NTH_BIT_IS_SET</span><span class="p">(</span><span class="n" style="color: #333;">neglectThose</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FALSE</span></span><span class="p">);</span></span>
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248
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"> <span class="n" style="color: #333;">extractQuadruplesRecursively</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nodep</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">quadruples</span><span class="p">,</span> <span class="n" style="color: #333;">neglectThose</span><span class="p">,</span> <span class="n" style="color: #333;">TRUE</span><span class="p">);</span></span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="c"> </span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="362" 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">@@ -362,6 +362,7 @@ int main(int argc, char *argv[])</td>
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">run_id</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'w'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* printf("optarg : %s\n", optarg); */</span></span>
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="c"> <span class="n" style="color: #333;">strcpy</span><span class="p">(</span><span class="n" style="color: #333;">workdir</span><span class="p">,</span> <span class="n" style="color: #333;">optarg</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="c"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="c"> <span class="k" style="font-weight: 600;">case</span> <span class="sc" style="color: #d14;">'x'</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -402,7 +403,9 @@ int main(int argc, char *argv[])</td>
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402
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="c"> <span class="n" style="color: #333;">PR</span><span class="p">(</span><span class="s" style="color: #d14;">"Something went wrong during tree initialisation. Sorry.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="c"> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="c"> <span class="p">}</span> </span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="c"> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">bitVectorLength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">GET_BITVECTOR_LENGTH</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="c"> <span class="n" style="color: #333;">calculateLeafStability</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">bootTrees</span><span class="p">,</span> <span class="n" style="color: #333;">excludeFile</span><span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#564056cc21f0e2f9f97b1e698e25cf7a4bd3915b"><strong>rnr-mast.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -208,7 +208,7 @@ BitVector*** getIntersectionOfRootedTriples(FILE *bootstrapFile, All *tr, int st</td>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> </span>
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">FOR_0_LIMIT</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">)</span></span>
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210
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">NOT</span> <span class="n" style="color: #333;">NTH_BIT_IS_SET</span><span class="p">(</span><span class="n" style="color: #333;">neglectThose</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">FALSE</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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212
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"> </span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* reset bit-vectors */</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">FOR_0_LIMIT</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="652" 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="652" 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">@@ -652,7 +652,7 @@ void verifyMasts(All *tr, FILE *bootstrapFile, BitVector *taxaToKeep)</td>
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652
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652
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* prune taxa */</span></span>
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653
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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654
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">NOT</span> <span class="p">(</span><span class="n" style="color: #333;">NTH_BIT_IS_SET</span><span class="p">(</span><span class="n" style="color: #333;">taxaToKeep</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">))</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC655" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;"><span class="idiff left">+</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC655" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FALSE</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="p">)</span></span>
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="c"> <span class="n" style="color: #333;">commonStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="701" 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="701" 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">@@ -701,7 +701,10 @@ void printMastToFile(All *tr, FILE *bootstrapFile, BitVector *mast, FILE *resul</td>
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701
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="c"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span></span>
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="c"> <span class="n" style="color: #333;">droppedTaxaNum</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> </span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="c"> <span class="n" style="color: #333;">tips</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifdef DEBUG</span></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="c"> <span class="n" style="color: #333;">tips</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="c"> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="c"> <span class="n" style="color: #333;">rewind</span><span class="p">(</span><span class="n" style="color: #333;">bootstrapFile</span><span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="c"> <span class="n" style="color: #333;">readBootstrapTree</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">bootstrapFile</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -709,12 +712,15 @@ void printMastToFile(All *tr, FILE *bootstrapFile, BitVector *mast, FILE *resul</td>
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">NOT</span> <span class="n" style="color: #333;">NTH_BIT_IS_SET</span><span class="p">(</span><span class="n" style="color: #333;">mast</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC714" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* printf("intending to prune: %d\n", i) ; */</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">FALSE</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="c"> <span class="n" style="color: #333;">droppedTaxaNum</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;"><span class="idiff left right">#ifdef DEBUG</span> </span></span>
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<pre style="margin: 0;"> <span id="LC721" class="line" lang="c"> <span class="n" style="color: #333;">tips</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countTips</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">countTips</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">start</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">back</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">);</span></span>
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717
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722
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<pre style="margin: 0;"> <span id="LC722" class="line" lang="c"> <span class="n" style="color: #333;">assert</span><span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">tips</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">)</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">droppedTaxaNum</span><span class="p">));</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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718
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724
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeTreeToString</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">FALSE</span><span class="p">);</span></span>
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719
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725
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<pre style="margin: 0;"> <span id="LC725" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="c"> <span class="n" style="color: #333;">printBothOpen</span><span class="p">(</span><span class="s" style="color: #d14;">"MAST tree: %s"</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#31bc0c7d7009021cf0b86050fdf205abf3c73a28"><strong>rnr-prune.c</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -40,7 +40,6 @@</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "common.h"</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "Tree.h"</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "List.h"</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "BitVector.h"</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">run_id</span><span class="p">[</span><span class="mi" style="color: #099;">128</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">workdir</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">masterTime</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">NumberOfThreads</span><span class="p">;</span> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -111,7 +109,7 @@ void pruneTaxaFromTreeset(char *bootstrapFileName, char *bestTreeFile, char *toD</td>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indicesToDrop</span><span class="p">;</span></span>
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113
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="c"> <span class="n" style="color: #333;">FOR_LIST</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p">);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">FALSE</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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115
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="c"></span>
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116
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeTreeToString</span><span class="p">(</span><span class="n" style="color: #333;">tr</span> <span class="p">,</span> <span class="n" style="color: #333;">FALSE</span><span class="p">);</span> </span>
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117
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" 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="127" 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">@@ -129,7 +127,7 @@ void pruneTaxaFromTreeset(char *bootstrapFileName, char *bestTreeFile, char *toD</td>
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129
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">readBestTree</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">bestTree</span><span class="p">);</span></span>
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130
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="c"> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indicesToDrop</span><span class="p">;</span></span>
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131
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="c"> <span class="n" style="color: #333;">FOR_LIST</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">index</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">TRUE</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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133
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writeTreeToString</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">TRUE</span><span class="p">);</span> </span>
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">outf</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">tmp</span><span class="p">);</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" 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="166" 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">@@ -168,7 +166,7 @@ int main(int argc, char *argv[])</td>
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168
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="c"> <span class="n" style="color: #333;">programVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PROG_VERSION</span><span class="p">;</span></span>
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169
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="c"> <span class="n" style="color: #333;">programReleaseDate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PROG_RELEASE_DATE</span><span class="p">;</span> </span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"hi:t:x:n:"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="c"> <span class="k" style="font-weight: 600;">while</span><span class="p">((</span><span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getopt</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"hi:t:x:n:<span class="idiff left right">w:</span>"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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172
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="c"> <span class="k" style="font-weight: 600;">switch</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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174
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="c"> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#13fe96832b46c053d9d1db4e3e3597afc55357ae"><strong>rnr-tii.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="208" 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="208" 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">@@ -208,7 +208,7 @@ void getTaxonomicInstability(All *tr, char *treesFileName, char *excludeFile)</td>
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208
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="c"> </span>
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209
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="c"> <span class="n" style="color: #333;">FOR_0_LIMIT</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">mxtips</span><span class="p">)</span></span>
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210
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span> <span class="n" style="color: #333;">NOT</span> <span class="n" style="color: #333;">NTH_BIT_IS_SET</span><span class="p">(</span><span class="n" style="color: #333;">neglectThose</span><span class="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">))</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="c"> <span class="n" style="color: #333;">pruneTaxon</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">FALSE</span></span><span class="p">);</span></span>
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212
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="c"></span>
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/* assert that we get the right labels */</span></span>
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="c"> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gatherDistances</span><span class="p">(</span><span class="n" style="color: #333;">tr</span><span class="p">,</span> <span class="n" style="color: #333;">tr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nodep</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">distances</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="n" style="color: #333;">TRUE</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#cd02ee1411f35dbba48aee4f1ac519a4be3e131f"><strong>sharedVariables.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,7 @@ pthread_mutex_t mutex;</td>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="c"></span>
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40
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">infoFileName</span><span class="p">,</span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="c"> <span class="n" style="color: #333;">run_id</span><span class="p">[</span><span class="mi" style="color: #099;">128</span><span class="p">],</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"> <span class="o" style="font-weight: 600;"><span class="idiff left right">*</span></span><span class="n" style="color: #333;">workdir</span><span class="p">,</span> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="n" style="color: #333;">workdir</span><span class="p"><span class="idiff left">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1024</span></span><span class="p"><span class="idiff right">]</span>,</span> </span>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">programName</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">programVersion</span><span class="p">,</span> </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">programReleaseDate</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/roguenarok/-/commit/db6f4ec9b3cb94d1b7af09cc9ed2be94940f4fa6#69e22c5499a98ab6a75ce802eb8a292d35297398"><strong>utils/pruneWrapper.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#! /bin/bash</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">PRUNE</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"../rnr-prune"</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">NUM</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$1</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">RNR_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$2</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">BS_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$3</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="nv" style="color: #008080;">TRE_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$4</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$# </span><span class="nt" style="color: #000080;">-lt</span> 3 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"This is a tiny helper script for obtaining pruned trees from a RogueNaRok search. </span><span class="se" style="color: #d14;">\n</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="s2" style="color: #d14;">Call it as follows:</span><span class="se" style="color: #d14;">\n</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="s2" style="color: #d14;">./pruneWrapper.sh <numToPrune> <RogueNaRok_droppedRogues-file> <bootstrap-tree-file> <ML-tree-file></span><span class="se" style="color: #d14;">\n</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="s2" style="color: #d14;">* <numToPrune> prune the first x rogues that RogueNaRok identified (the order in the output is important). </span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> If you want to prune all rogues as identified by RogueNaRok, simply enter an arbitrarily large number in this position </span><span class="se" style="color: #d14;">\n</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="s2" style="color: #d14;">* further arguments are self-explainatory.</span><span class="se" style="color: #d14;">\n</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="s2" style="color: #d14;">* output is written to stdout</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">id</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$RNR_FILE</span> |awk <span class="nt" style="color: #000080;">-F</span> <span class="nb" style="color: #0086b3;">.</span> <span class="s1" style="color: #d14;">'{print $NF}'</span><span class="si" style="color: #d14;">)</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nv" style="color: #008080;">excludeFile</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$id</span>.<span class="nv" style="color: #008080;">$NUM</span>.exclude</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="nv" style="color: #008080;">$RNR_FILE</span> | <span class="nb" style="color: #0086b3;">tail</span> <span class="nt" style="color: #000080;">-n</span> +3 | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n</span> <span class="nv" style="color: #008080;">$NUM</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-f</span> 3 <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$excludeFile</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"></span>
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<td class="new_line diff-line-num new" 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="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$TRE_FILE</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nv" style="color: #008080;">$PRUNE</span> <span class="nt" style="color: #000080;">-x</span> <span class="nv" style="color: #008080;">$excludeFile</span> <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$BS_FILE</span> <span class="nt" style="color: #000080;">-n</span> <span class="nv" style="color: #008080;">$id</span> <span class="o" style="font-weight: 600;">></span> /dev/null</span>
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">==</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"wrote file RnR-prune_prunedBootstraps.</span><span class="nv" style="color: #008080;">$id</span><span class="s2" style="color: #d14;">"</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"something went wrong, maybe file RnR-prune_prunedBootstraps.</span><span class="nv" style="color: #008080;">$id</span><span class="s2" style="color: #d14;"> already exists (delete it to re-run)"</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"> <span class="nv" style="color: #008080;">$PRUNE</span> <span class="nt" style="color: #000080;">-x</span> <span class="nv" style="color: #008080;">$excludeFile</span> <span class="nt" style="color: #000080;">-i</span> <span class="nv" style="color: #008080;">$BS_FILE</span> <span class="nt" style="color: #000080;">-t</span> <span class="nv" style="color: #008080;">$TRE_FILE</span> <span class="nt" style="color: #000080;">-n</span> <span class="nv" style="color: #008080;">$id</span> <span class="o" style="font-weight: 600;">></span> /dev/null</span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nv" style="color: #008080;">$?</span> <span class="o" style="font-weight: 600;">==</span> 0 <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="new_line diff-line-num new" 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="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"wrote file RnR-prune_prunedBootstraps.</span><span class="nv" style="color: #008080;">$id</span><span class="s2" style="color: #d14;"> and RnR-prune_prunedBestTree.</span><span class="nv" style="color: #008080;">$id</span><span class="s2" style="color: #d14;">"</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"something went wrong, maybe file RnR-prune_prunedBootstraps.</span><span class="nv" style="color: #008080;">$id</span><span class="s2" style="color: #d14;"> or RnR-prune_prunedBestTree.</span><span class="nv" style="color: #008080;">$id</span><span class="s2" style="color: #d14;"> already exist (delete them to re-run)"</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"></span></pre>
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