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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/iqtree">Debian Med / iqtree</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662">48b7c97f</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-01-02T13:13:29Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.6.9+dfsg</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#1d1fdc052f5fcf9ab26c74024f124949c4236777">
alignment/superalignment.cpp
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<li class="file-stats">
<a href="#eeabe52528589e25f9b2f08c57e0366718a2612b">
nclextra/msetsblock.cpp
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<li class="file-stats">
<a href="#21e4b332fdf0686440453fe0e29b2cbf3a8eaa54">
nclextra/msetsblock.h
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<li class="file-stats">
<a href="#e87660aa23195472e9f90c6a5bf62987138cacf8">
tree/iqtree.cpp
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<li class="file-stats">
<a href="#0c95698e73a930bf5364a771c4515cc61daa4d26">
utils/checkpoint.cpp
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<li class="file-stats">
<a href="#1227c902f85851ac68420863692a74bbc933e561">
utils/tools.cpp
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<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="51" 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">@@ -51,7 +51,7 @@ add_definitions(-DIQ_TREE)</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The version number.</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_MAJOR 1<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_MINOR 6<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">8</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_PATCH <span class="s2" style="color: #d14;">"<span class="idiff left right">9</span>"</span><span class="p">)</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC55" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>BUILD_SHARED_LIBS OFF<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cmake"></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">IQ-TREE</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/bqminh/IQ-TREE.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/bqminh/IQ-TREE)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">![License: GPL v2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v2-blue.svg</span><span class="p">)</span>](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">Efficient and versatile phylogenomic software by maximum likelihood <span class="nv" style="color: teal;"><http://www.iqtree.org></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #999;">Introduction</span></span>
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<li id="1d1fdc052f5fcf9ab26c74024f124949c4236777">
<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#1d1fdc052f5fcf9ab26c74024f124949c4236777"><strong>alignment/superalignment.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1008" 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="1008" 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">@@ -1008,7 +1008,10 @@ void SuperAlignment::createBootstrapAlignment(int *pattern_freq, const char *spe</td>
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1008
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<pre style="margin: 0;"> <span id="LC1008" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// resampling sites within genes</span></span>
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1009
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1009
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<pre style="margin: 0;"> <span id="LC1009" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">offset</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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1010
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1010
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<pre style="margin: 0;"> <span id="LC1010" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Alignment</span><span class="o" style="font-weight: 600;">*>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partitions</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">partitions</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1011
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<pre style="margin: 0;">-<span id="LC1011" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">createBootstrapAlignment</span><span class="p">(</span><span class="n" style="color: #333;">pattern_freq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">rstream</span><span class="p">);</span></span>
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1011
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<pre style="margin: 0;">+<span id="LC1011" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="s" style="color: #d14;">"SCALE="</span><span class="p">,</span> <span class="mi" style="color: #099;">6</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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1012
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<pre style="margin: 0;">+<span id="LC1012" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">createBootstrapAlignment</span><span class="p">(</span><span class="n" style="color: #333;">pattern_freq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">rstream</span><span class="p">);</span></span>
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1013
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<pre style="margin: 0;">+<span id="LC1013" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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1014
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<pre style="margin: 0;">+<span id="LC1014" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">createBootstrapAlignment</span><span class="p">(</span><span class="n" style="color: #333;">pattern_freq</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">rstream</span><span class="p">);</span></span>
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1012
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1015
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<pre style="margin: 0;"> <span id="LC1015" class="line" lang="cpp"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getNPattern</span><span class="p">();</span></span>
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1013
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1016
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<pre style="margin: 0;"> <span id="LC1016" class="line" lang="cpp"> <span class="p">}</span></span>
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1014
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1017
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<pre style="margin: 0;"> <span id="LC1017" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1259" 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">@@ -1259,11 +1262,12 @@ Alignment *SuperAlignment::concatenateAlignments(set<int> &ids) {</td>
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1259
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1262
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<pre style="margin: 0;"> <span id="LC1262" class="line" lang="cpp"></span>
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1260
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1263
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<pre style="margin: 0;"> <span id="LC1263" class="line" lang="cpp"><span class="n" style="color: #333;">Alignment</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">SuperAlignment</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">concatenateAlignments</span><span class="p">()</span> <span class="p">{</span></span>
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1261
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1264
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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">SeqType</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seq_types</span><span class="p">;</span></span>
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1265
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<pre style="margin: 0;">+<span id="LC1265" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</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;">genetic_codes</span><span class="p">;</span></span>
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1262
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1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">ids</span><span class="p">;</span></span>
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1263
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1267
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<pre style="margin: 0;"> <span id="LC1267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</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;">partitions</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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1264
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1268
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1265
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1269
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seq_types</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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1266
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<pre style="margin: 0;">-<span id="LC1266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">partitions</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;">seq_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq_types</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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1270
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<pre style="margin: 0;">+<span id="LC1270" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">partitions</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;">seq_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">seq_types</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">]</span><span class="idiff left"> </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">partitions</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">genetic_code</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">genetic_codes</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">j</span></span><span class="p"><span class="idiff right">]</span>)</span> <span class="p">{</span></span>
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1267
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1271
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<pre style="margin: 0;"> <span id="LC1271" class="line" lang="cpp"> <span class="n" style="color: #333;">ids</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1268" 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">
1268
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1272
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<pre style="margin: 0;"> <span id="LC1272" class="line" lang="cpp"> <span class="n" style="color: #333;">found</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1269" 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">
1269
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<td class="diff-line-num new_line" data-linenumber="1273" 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">
1273
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<pre style="margin: 0;"> <span id="LC1273" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1272" 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="1276" 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">@@ -1272,6 +1276,7 @@ Alignment *SuperAlignment::concatenateAlignments() {</td>
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1272
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1276
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<pre style="margin: 0;"> <span id="LC1276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1273
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1277
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<pre style="margin: 0;"> <span id="LC1277" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// create a new partition</span></span>
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1274
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1278
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<pre style="margin: 0;"> <span id="LC1278" class="line" lang="cpp"> <span class="n" style="color: #333;">seq_types</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">partitions</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;">seq_type</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1279" 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">
1279
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"> <span class="n" style="color: #333;">genetic_codes</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">partitions</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;">genetic_code</span><span class="p">);</span></span>
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1275
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1280
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="cpp"> <span class="n" style="color: #333;">ids</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">set</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span><span class="p">());</span></span>
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1276
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1281
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<pre style="margin: 0;"> <span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;">ids</span><span class="p">.</span><span class="n" style="color: #333;">back</span><span class="p">().</span><span class="n" style="color: #333;">insert</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">);</span></span>
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1277
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1282
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="eeabe52528589e25f9b2f08c57e0366718a2612b">
<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#eeabe52528589e25f9b2f08c57e0366718a2612b"><strong>nclextra/msetsblock.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" 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">@@ -267,6 +267,9 @@ void MSetsBlock::Read(NxsToken &token)</td>
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267
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"></span>
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268
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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269
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"> <span class="p">{</span></span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">errormsg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Unknown command "</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">errormsg</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">token</span><span class="p">.</span><span class="n" style="color: #333;">GetToken</span><span class="p">();</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">NxsException</span><span class="p">(</span><span class="n" style="color: #333;">errormsg</span><span class="p">,</span> <span class="n" style="color: #333;">token</span><span class="p">.</span><span class="n" style="color: #333;">GetFilePosition</span><span class="p">(),</span> <span class="n" style="color: #333;">token</span><span class="p">.</span><span class="n" style="color: #333;">GetFileLine</span><span class="p">(),</span> <span class="n" style="color: #333;">token</span><span class="p">.</span><span class="n" style="color: #333;">GetFileColumn</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">SkippingCommand</span><span class="p">(</span><span class="n" style="color: #333;">token</span><span class="p">.</span><span class="n" style="color: #333;">GetToken</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <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">@@ -284,6 +287,11 @@ void MSetsBlock::Read(NxsToken &token)</td>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">MSetsBlock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SkippingCommand</span><span class="p">(</span><span class="n" style="color: #333;">NxsString</span> <span class="n" style="color: #333;">commandName</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"WARNING: Skipping unknown command "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">commandName</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"><span class="n" style="color: #333;">CharSet</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">MSetsBlock</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">findCharSet</span><span class="p">(</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CharSet</span><span class="o" style="font-weight: 600;">*>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">charsets</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">charsets</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#21e4b332fdf0686440453fe0e29b2cbf3a8eaa54"><strong>nclextra/msetsblock.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">@@ -95,6 +95,12 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Reset</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> called when some commands are skipped</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @param commandName command name</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">SkippingCommand</span><span class="p">(</span><span class="n" style="color: #333;">NxsString</span> <span class="n" style="color: #333;">commandName</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> @return the number of sets</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#e87660aa23195472e9f90c6a5bf62987138cacf8"><strong>tree/iqtree.cpp</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">@@ -2885,6 +2885,15 @@ void IQTree::refineBootTrees() {</td>
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<pre style="margin: 0;"> <span id="LC2885" class="line" lang="cpp"> <span class="n" style="color: #333;">finish_random</span><span class="p">();</span></span>
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2886
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2886
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<pre style="margin: 0;"> <span id="LC2886" class="line" lang="cpp"> <span class="n" style="color: #333;">randstream</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saved_randstream</span><span class="p">;</span></span>
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2887
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<pre style="margin: 0;"> <span id="LC2887" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC2888" class="line" lang="cpp"> <span class="n" style="color: #333;">SplitGraph</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sg</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">SplitGraph</span><span class="p">;</span></span>
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2889
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<pre style="margin: 0;">+<span id="LC2889" class="line" lang="cpp"> <span class="n" style="color: #333;">summarizeBootstrap</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">sg</span><span class="p">);</span></span>
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2890
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<pre style="margin: 0;">+<span id="LC2890" class="line" lang="cpp"> <span class="n" style="color: #333;">sg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">removeTrivialSplits</span><span class="p">();</span></span>
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2891
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<pre style="margin: 0;">+<span id="LC2891" class="line" lang="cpp"> <span class="n" style="color: #333;">sg</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">setCheckpoint</span><span class="p">(</span><span class="n" style="color: #333;">checkpoint</span><span class="p">);</span></span>
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2892
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<pre style="margin: 0;">+<span id="LC2892" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_splits</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">sg</span><span class="p">);</span></span>
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2893
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<pre style="margin: 0;">+<span id="LC2893" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC2894" class="line" lang="cpp"> <span class="n" style="color: #333;">saveCheckpoint</span><span class="p">();</span></span>
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2895
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<pre style="margin: 0;">+<span id="LC2895" class="line" lang="cpp"> <span class="n" style="color: #333;">checkpoint</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">dump</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC2896" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC2897" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// restore</span></span>
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2889
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<pre style="margin: 0;"> <span id="LC2898" class="line" lang="cpp"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">gbo_replicates</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_trees</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC2899" class="line" lang="cpp"> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nni_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">saved_nni_type</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4051" 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">@@ -4051,6 +4060,8 @@ void IQTree::printResultTree(ostream &out) {</td>
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4051
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4060
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<pre style="margin: 0;"> <span id="LC4060" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">IQTree</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">printBestCandidateTree</span><span class="p">()</span> <span class="p">{</span></span>
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4052
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4061
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<pre style="margin: 0;"> <span id="LC4061" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">MPIHelper</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInstance</span><span class="p">().</span><span class="n" style="color: #333;">isWorker</span><span class="p">())</span></span>
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4053
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4062
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<pre style="margin: 0;"> <span id="LC4062" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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4063
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<pre style="margin: 0;">+<span id="LC4063" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">suppress_output_flags</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">OUT_TREEFILE</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4064" 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">
4064
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<pre style="margin: 0;">+<span id="LC4064" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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4054
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<td class="diff-line-num new_line" data-linenumber="4065" 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">
4065
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<pre style="margin: 0;"> <span id="LC4065" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tree_file_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">out_prefix</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="4055" 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">
4055
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4066
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<pre style="margin: 0;"> <span id="LC4066" class="line" lang="cpp"> <span class="n" style="color: #333;">tree_file_name</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">".treefile"</span><span class="p">;</span></span>
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4056
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4067
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<pre style="margin: 0;"> <span id="LC4067" class="line" lang="cpp"> <span class="n" style="color: #333;">readTreeString</span><span class="p">(</span><span class="n" style="color: #333;">candidateTrees</span><span class="p">.</span><span class="n" style="color: #333;">getBestTreeStrings</span><span class="p">(</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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<li id="0c95698e73a930bf5364a771c4515cc61daa4d26">
<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#0c95698e73a930bf5364a771c4515cc61daa4d26"><strong>utils/checkpoint.cpp</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">@@ -9,6 +9,7 @@</td>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tools.h"</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "timeutil.h"</span></span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "gzstream.h"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstdio></span></span>
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12
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</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;">CKP_HEADER</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--- # IQ-TREE Checkpoint ver >= 1.6"</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</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;">CKP_HEADER_OLD</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"--- # IQ-TREE Checkpoint"</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>
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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">@@ -149,12 +150,18 @@ void Checkpoint::dump(bool force) {</td>
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149
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="p">}</span></span>
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151
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">prev_dump_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getRealTime</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">filename_tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".tmp"</span><span class="p">;</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fileExists</span><span class="p">(</span><span class="n" style="color: #333;">filename_tmp</span><span class="p">))</span> <span class="p">{</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">outWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"IQ-TREE was killed while writing temporary checkpoint file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename_tmp</span><span class="p">);</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">outWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"You should increase checkpoint interval from the default 60 seconds"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">outWarning</span><span class="p">(</span><span class="s" style="color: #d14;">"via -cptime option to avoid too frequent checkpoint for large datasets"</span><span class="p">);</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="p">}</span></span>
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152
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</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="cpp"> <span class="n" style="color: #333;">ostream</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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154
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<td class="diff-line-num new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">compression</span><span class="p">)</span> </span>
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155
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<td class="diff-line-num new_line old" data-linenumber="162" 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="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ogzstream</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ogzstream</span><span class="p">(</span><span class="n" style="color: #333;">filename<span class="idiff left right">_tmp</span></span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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156
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff">());</span></span><span class="idiff right"> </span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">ofstream</span><span class="p">(</span><span class="n" style="color: #333;">filename<span class="idiff left">_tmp</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">c_str</span></span><span class="p"><span class="idiff right">());</span></span></span>
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158
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cpp"> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">exceptions</span><span class="p">(</span><span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">failbit</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">badbit</span><span class="p">);</span></span>
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159
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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160
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// call dump stream</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="165" 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="172" 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">@@ -165,6 +172,12 @@ void Checkpoint::dump(bool force) {</td>
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165
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="p">((</span><span class="n" style="color: #333;">ofstream</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">out</span><span class="p">)</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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166
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span> <span class="n" style="color: #333;">out</span><span class="p">;</span></span>
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167
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cout << "Checkpoint dumped" << endl;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">fileExists</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</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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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">outError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot remove file "</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">rename</span><span class="p">(</span><span class="n" style="color: #333;">filename_tmp</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</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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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">outError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot rename file "</span><span class="p">,</span> <span class="n" style="color: #333;">filename_tmp</span><span class="p">);</span></span>
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168
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<td class="diff-line-num new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">ios</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">failure</span> <span class="o" style="font-weight: 600;">&</span><span class="p">)</span> <span class="p">{</span></span>
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169
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">outError</span><span class="p">(</span><span class="n" style="color: #333;">ERR_WRITE_OUTPUT</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="170" 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">
170
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="1227c902f85851ac68420863692a74bbc933e561">
<a href="https://salsa.debian.org/med-team/iqtree/commit/48b7c97f2de5b926ed28e09c26a5076e769cc662#1227c902f85851ac68420863692a74bbc933e561"><strong>utils/tools.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1707" 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="1707" 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">@@ -1707,7 +1707,7 @@ void parseArg(int argc, char *argv[], Params ¶ms) {</td>
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1707
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1707
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<pre style="margin: 0;"> <span id="LC1707" class="line" lang="cpp"> <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;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cnt</span><span class="p">],</span> <span class="s" style="color: #d14;">"-rclusterf"</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="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1708" 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">
1708
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1708
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<pre style="margin: 0;"> <span id="LC1708" class="line" lang="cpp"> <span class="n" style="color: #333;">cnt</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1709" 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">
1709
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<td class="diff-line-num new_line" data-linenumber="1709" 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">
1709
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<pre style="margin: 0;"> <span id="LC1709" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">cnt</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">argc</span><span class="p">)</span></span>
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1710
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<td class="diff-line-num new_line old" data-linenumber="1710" 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="LC1710" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="s" style="color: #d14;">"Use -rcluster <percent>"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1710
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<pre style="margin: 0;">+<span id="LC1710" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="s" style="color: #d14;">"Use -rcluster<span class="idiff left right">f</span> <percent>"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1711" 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">
1711
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1711
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<pre style="margin: 0;"> <span id="LC1711" class="line" lang="cpp"> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">partfinder_rcluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">convert_double</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cnt</span><span class="p">]);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1712" 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">
1712
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1712
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<pre style="margin: 0;"> <span id="LC1712" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">partfinder_rcluster</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;">params</span><span class="p">.</span><span class="n" style="color: #333;">partfinder_rcluster</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1713" 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">
1713
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1713
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<pre style="margin: 0;"> <span id="LC1713" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="s" style="color: #d14;">"rcluster percentage must be between 0 and 100"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1722" 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="1722" 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">@@ -1722,6 +1722,8 @@ void parseArg(int argc, char *argv[], Params ¶ms) {</td>
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1722
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1722
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<pre style="margin: 0;"> <span id="LC1722" class="line" lang="cpp"> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">partfinder_rcluster_max</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">convert_int</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">cnt</span><span class="p">]);</span></span>
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1723
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1723
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<pre style="margin: 0;"> <span id="LC1723" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">partfinder_rcluster_max</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1724" 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">
1724
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1724
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<pre style="margin: 0;"> <span id="LC1724" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="s" style="color: #d14;">"rcluster-max must be between > 0"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1725" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">partfinder_rcluster</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1726" class="line" lang="cpp"> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">partfinder_rcluster</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">99.9999</span><span class="p">;</span></span>
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1725
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<td class="diff-line-num new_line" data-linenumber="1727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC1727" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1726
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<pre style="margin: 0;"> <span id="LC1728" class="line" lang="cpp"> <span class="p">}</span></span>
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1727
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1729
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="cpp"></span>
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