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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/clonalframeml">Debian Med / clonalframeml</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16">81343d66</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-02-27T11:28:26+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.12</pre>
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<h4>20 changed files:</h4>
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.gitignore
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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src/README.txt
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src/brent.h
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src/coalesce/coalescent_record.h
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src/main.cpp
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src/main.h
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src/make.sh
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src/makefile
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src/myutils/DNA.h
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src/myutils/argumentwizard.h
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src/myutils/matrix.h
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src/myutils/mydouble.h
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src/myutils/myutils.h
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src/myutils/newick.h
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src/myutils/random.h
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src/myutils/vector.h
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src/powell.h
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src/xmfa.h
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">src/ClonalFrameML</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">src/main.o</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">src/version.h</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">src/main</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">src/.vscode/*</span></pre>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #999;"># Introduction #</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">This is the homepage of ClonalFrameML, a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by <span class="p">[</span><span class="nv" style="color: #008080;">Xavier Didelot</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">www.imperial.ac.uk/medicine/people/x.didelot/</span></span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">Daniel Wilson</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.danielwilson.me.uk/</span><span class="p">)</span>. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">This is the homepage of ClonalFrameML, a software package that performs efficient inference of recombination in bacterial genomes. ClonalFrameML was created by <span class="p">[</span><span class="nv" style="color: #008080;">Xavier Didelot</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">xavierdidelot.github.io</span></span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: #008080;">Daniel Wilson</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.danielwilson.me.uk/</span><span class="p">)</span>. ClonalFrameML can be applied to any type of aligned sequence data, but is especially aimed at analysis of whole genome sequences. It is able to compare hundreds of whole genomes in a matter of hours on a standard Desktop computer. There are three main outputs from a run of ClonalFrameML: a phylogeny with branch lengths corrected to account for recombination, an estimation of the key parameters of the recombination process, and a genomic map of where recombination took place for each branch of the phylogeny.</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">ClonalFrameML is a maximum likelihood implementation of the Bayesian software <span class="p">[</span><span class="nv" style="color: #008080;">ClonalFrame</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">www.xavierdidelot.xtreemhost.com/clonalframe.htm</span></span><span class="p">)</span> which was previously described by <span class="p">[</span><span class="nv" style="color: #008080;">Didelot and Falush (2007)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.genetics.org/cgi/content/abstract/175/3/1251</span><span class="p">)</span>. The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues. A scientific paper describing ClonalFrameML in detail has been published, see <span class="p">[</span><span class="nv" style="color: #008080;">Didelot X, Wilson DJ (2015) ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Comput Biol 11(2): e1004041. doi:10.1371/journal.pcbi.1004041</span><span class="p">](</span><span class="sx" style="color: #d14;">http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004041</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">ClonalFrameML is a maximum likelihood implementation of the Bayesian software <span class="p">[</span><span class="nv" style="color: #008080;">ClonalFrame</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">xavierdidelot.github.io/clonalframe.html</span></span><span class="p">)</span> which was previously described by <span class="p">[</span><span class="nv" style="color: #008080;">Didelot and Falush (2007)</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.genetics.org/cgi/content/abstract/175/3/1251</span><span class="p">)</span>. The recombination model underpinning ClonalFrameML is exactly the same as for ClonalFrame, but this new implementation is a lot faster, is able to deal with much larger genomic dataset, and does not suffer from MCMC convergence issues. A scientific paper describing ClonalFrameML in detail has been published, see <span class="p">[</span><span class="nv" style="color: #008080;">Didelot X, Wilson DJ (2015) ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. PLoS Comput Biol 11(2): e1004041. doi:10.1371/journal.pcbi.1004041</span><span class="p">](</span><span class="sx" style="color: #d14;">http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004041</span><span class="p">)</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;"># Download and Installation #</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">@@ -30,4 +30,4 @@ The user guide for ClonalFrameML is available [here](https://github.com/xavierdi</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="gh" style="color: #999;"># Getting help #</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">If you need assistance using ClonalFrameML, you can get in touch by emailing either <span class="p">[</span><span class="nv" style="color: #008080;">Xavier Didelot</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">www.xavierdidelot.xtreemhost.com/contact.htm</span></span><span class="p">)</span> or <span class="p">[</span><span class="nv" style="color: #008080;">Daniel Wilson</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.danielwilson.me.uk/contact.html</span><span class="p">)</span>.</span></pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">If you need assistance using ClonalFrameML, you can get in touch by emailing either <span class="p">[</span><span class="nv" style="color: #008080;">Xavier Didelot</span><span class="p">](</span><span class="sx" style="color: #d14;">http://<span class="idiff left right">xavierdidelot.github.io/contact.html</span></span><span class="p">)</span> or <span class="p">[</span><span class="nv" style="color: #008080;">Daniel Wilson</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.danielwilson.me.uk/contact.html</span><span class="p">)</span>.</span></pre>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#22057da97759a9e1ffb6b143fbc60856e9906161"><strong>src/README.txt</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ClonalFrameML</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Xavier Didelot and Daniel Wilson. 2015</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">This program reads in a Newick tree and FASTA file and, for all variable sites, reconstructs</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">the joint maximum likelihood sequences at all nodes (including, for the purposes of imputation, tips)</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">using the HKY85 nucleotide substitution model and an algorithm described in:</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> Tal Pupko, Itsik Peer, Ron Shamir, and Dan Graur. Mol. Biol. Evol. 17(6):890–896. 2000</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Branch lengths of the tree are corrected for heterospecific horizontal gene transfer using a new maximum-</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">likelihood algorithm implementing the ClonalFrame model that was described in:</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> Inference of Bacterial Microevolution Using Multilocus Sequence Data</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> Xavier Didelot, and Daniel Falush. Genetics 175(3):1251-1266. 2007</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Syntax: ClonalFrameML newick_file fasta_file output_file [OPTIONS]</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">newick_file The tree specified in Newick format. It must be an unrooted bifurcating tree. All</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> tips should be uniquely labelled and the internal nodes must not be labelled. Note that the</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> branch lengths must be scaled in units of expected number of substitutions per site.</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> Failure to provide appropriately scaled branch lengths will adversely affect results.</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">fasta_file The nucleotide sequences specified in FASTA format, with labels exactly matching those in</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> the newick_file. The letter codes A, C, G and T are interpreted directly, U is converted</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> to T, and N, -, ? and X are treated equivalently as ambiguity codes. No other codes are</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> allowed.</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">output_file The prefix for the output files, described below.</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">[OPTIONS] Run ClonalFrameML with no arguments to see the options available.</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">The program reports the empirical nucleotide frequencies and the joint log-likelihood of the reconstructed</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">sequences for variable sites. Files are output with the following suffixes:</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">.labelled_tree.newick The corrected Newick tree is ouput with internal nodes labelled so that they</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> correspond with the reconstructed ancestral sequence file.</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">.ML_sequence.fasta The reconstructed sequences (ancestral and, for the purposes of imputation,</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> observed) in FASTA format with letter codes A, C, G and T only. The labels</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> match exactly those in the output Newick tree.</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">.position_cross_reference.txt A vector of comma-separated values equal in length to the input FASTA file</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> relating the positions of (variable) sites in the input FASTA file to the</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> positions of their reconstructed sequences in the output FASTA file, starting</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> with position 1. Sites in the input file not reconstructed are assigned a 0.</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">.importation_status.txt A FASTA file representing the inferred importation status of every site</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> coded as 0 (unimported) 1 (imported) 2 (unimported homoplasy/multiallelic)</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> 3 (imported homoplasy/multiallelic) 4 (untested compatible) 5 (untested</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> homoplasy).</span></pre>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#656920c9413167755393d22094054b141b9e3110"><strong>src/brent.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* Copyright 2013 Daniel Wilson.</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* </span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * brent.h</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part of ClonalFrameML</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">The myutils library</span> is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">ClonalFrameML</span> is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU Lesser General Public License as published by</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">The myutils library</span> is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">ClonalFrameML</span> is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * GNU Lesser General Public License for more details.</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU Lesser General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * along with <span class="idiff left right">the myutils library</span>. If not, see <http://www.gnu.org/licenses/>.</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * along with <span class="idiff left right">ClonalFrameML</span>. If not, see <http://www.gnu.org/licenses/>.</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Parts of this code are based on code in Numerical Recipes in C++</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * WH Press, SA Teukolsky, WT Vetterling, BP Flannery (2002).</span></span>
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<li id="cf0463c3e6aab6c84c18c7ddb6ce6a920df93e9b">
<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#cf0463c3e6aab6c84c18c7ddb6ce6a920df93e9b"><strong>src/coalesce/coalescent_record.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">@@ -3,18 +3,18 @@</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * coalescent_record.h</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part of the coalesce library.</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The <span class="idiff left right">myutils</span> library is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The <span class="idiff left right">coalesce</span> library is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU Lesser General Public License as published by</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The <span class="idiff left right">myutils</span> library is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * The <span class="idiff left right">coalesce</span> library is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * GNU Lesser General Public License for more details.</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU Lesser General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * along with the <span class="idiff left right">myutils</span> library. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * along with the <span class="idiff left right">coalesce</span> library. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _RECORD_H_</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define _RECORD_H_</span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#b958235ee8db37bcaceda04b6d55553b450c2db4"><strong>src/main.cpp</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* Copyright 2013 Daniel Wilson and Xavier Didelot.</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* </span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * main.cpp</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part of ClonalFrameML</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</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">@@ -21,7 +20,8 @@</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span> <span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <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;">argv</span><span class="p">[])</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">clock_t</span> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">clock</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC24" 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;">"ClonalFrameML "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ClonalFrameML_GITRevision</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="LC23" 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;">"ClonalFrameML "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ClonalFrameML_version</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="LC24" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</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="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"-version"</span><span class="p">)</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;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="s" style="color: #d14;">"-v"</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="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Process the command line arguments </span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="o" style="font-weight: 600;"><</span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</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">@@ -43,7 +43,6 @@ int main (const int argc, const char* argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-chromosome_name name, eg </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">chr</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> Output importation status file in BED format using given chromosome name."</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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44
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-min_branch_length value > 0 (default 1e-7) Minimum branch length."</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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45
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-reconstruct_invariant_sites true or false (default) Reconstruct the ancestral states at invariant sites."</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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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// errTxt << "-compress_reconstructed_sites true (default) or false Reduce the number of columns in the output FASTA file." << endl; // Alternative not currently implemented, so not optional</span></span>
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47
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-label_uncorrected_tree true or false (default) Regurgitate the uncorrected Newick tree with internal nodes labelled."</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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48
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Options affecting -em and -embranch:"</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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49
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-prior_mean df </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">0.1 0.001 0.1 0.0001</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> Prior mean for R/theta, 1/delta, nu and M."</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" 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="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">@@ -52,10 +51,12 @@ int main (const int argc, const char* argv[]) {</td>
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52
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-guess_initial_m true (default) or false Initialize M and nu jointly in the EM algorithms."</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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53
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52
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-emsim value >= 0 (default 0) Number of simulations to estimate uncertainty in the EM results."</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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54
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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-embranch_dispersion value > 0 (default .01) Dispersion in parameters among branches in the -embranch model."</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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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-output_filtered true of false (default) Output a filtered alignment including only non-recombinant sites."</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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55
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55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Options affecting -rescale_no_recombination:"</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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56
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-brent_tolerance tolerance (default .001) Set the tolerance of the Brent routine for -rescale_no_recombination."</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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57
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"-powell_tolerance tolerance (default .001) Set the tolerance of the Powell routine for -rescale_no_recombination."</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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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</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="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</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="n" style="color: #333;">endl</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> <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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59
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Process required arguments</span></span>
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<pre style="margin: 0;"> <span id="LC62" 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;">newick_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</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="64" 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="65" 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">@@ -64,6 +65,7 @@ int main (const int argc, const char* argv[]) {</td>
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64
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<td class="diff-line-num new_line" data-linenumber="65" 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">
65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tree_out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".labelled_tree.newick"</span><span class="p">;</span></span>
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65
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<td class="diff-line-num new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">oritree_out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".labelled_uncorrected_tree.newick"</span><span class="p">;</span></span>
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66
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<td class="diff-line-num new_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fasta_out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".ML_sequence.fasta"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fasta_filtered_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".filtered.fasta"</span><span class="p">;</span></span>
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67
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<td class="diff-line-num new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">xref_out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".position_cross_reference.txt"</span><span class="p">;</span></span>
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68
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">import_out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".importation_status.txt"</span><span class="p">;</span></span>
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69
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<td class="diff-line-num new_line" data-linenumber="71" 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">
71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">em_out_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".em.txt"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" 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="75" 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">@@ -73,7 +75,8 @@ int main (const int argc, const char* argv[]) {</td>
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73
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<td class="diff-line-num new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">case_sensitive</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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74
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<td class="diff-line-num new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">fasta_file_list</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="n" style="color: #333;">xmfa_file</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="n" style="color: #333;">imputation_only</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_incomplete_sites</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_user_sites</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="n" style="color: #333;">reconstruct_invariant_sites</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">;</span></span>
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75
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<td class="diff-line-num new_line" data-linenumber="77" 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">
77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">use_incompatible_sites</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"true"</span><span class="p">,</span> <span class="n" style="color: #333;">rescale_no_recombination</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="76" 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">
76
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<td class="diff-line-num new_line old" data-linenumber="78" 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="LC76" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">show_progress</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="n" style="color: #333;">compress_reconstructed_sites</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"true"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">show_progress</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">output_filtered</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">;</span></span>
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77
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<td class="diff-line-num new_line" data-linenumber="80" 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">
80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">string_prior_mean</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.1 0.001 0.1 0.0001"</span><span class="p">,</span> <span class="n" style="color: #333;">string_prior_sd</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"0.1 0.001 0.1 0.0001"</span><span class="p">,</span> <span class="n" style="color: #333;">string_initial_values</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.1 0.001 0.05"</span><span class="p">;</span></span>
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78
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<td class="diff-line-num new_line" data-linenumber="81" 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">
81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">guess_initial_m</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"true"</span><span class="p">,</span> <span class="n" style="color: #333;">em</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"true"</span><span class="p">,</span> <span class="n" style="color: #333;">embranch</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="n" style="color: #333;">label_original_tree</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"false"</span><span class="p">,</span> <span class="n" style="color: #333;">chr_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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79
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">brent_tolerance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0e-3</span><span class="p">,</span> <span class="n" style="color: #333;">powell_tolerance</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0e-3</span><span class="p">,</span> <span class="n" style="color: #333;">global_min_branch_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0e-7</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="92" 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="95" 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">@@ -92,7 +95,6 @@ int main (const int argc, const char* argv[]) {</td>
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<td class="diff-line-num old_line" data-linenumber="92" 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">
92
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<td class="diff-line-num new_line" data-linenumber="95" 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">
95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"powell_tolerance"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_DOUBLE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">powell_tolerance</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="93" 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">
93
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<td class="diff-line-num new_line" data-linenumber="96" 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">
96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"rescale_no_recombination"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_STRING</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">rescale_no_recombination</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="94" 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">
94
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<td class="diff-line-num new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"show_progress"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_STRING</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">show_progress</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="95" 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">
95
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<td class="diff-line-num new_line old" data-linenumber="98" 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="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"compress_reconstructed_sites"</span><span class="p">,</span><span class="n" style="color: #333;">TP_STRING</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compress_reconstructed_sites</span><span class="p">);</span> </span>
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<td class="diff-line-num old_line" data-linenumber="96" 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">
96
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<td class="diff-line-num new_line" data-linenumber="98" 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">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"min_branch_length"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_DOUBLE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">global_min_branch_length</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="97" 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">
97
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<td class="diff-line-num new_line" data-linenumber="99" 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">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"prior_mean"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_STRING</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">string_prior_mean</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="98" 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">
98
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<td class="diff-line-num new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"prior_sd"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_STRING</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">string_prior_sd</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="106" 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">@@ -104,6 +106,7 @@ int main (const int argc, const char* argv[]) {</td>
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<td class="diff-line-num old_line" data-linenumber="104" 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">
104
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<td class="diff-line-num new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"embranch_dispersion"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_DOUBLE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">embranch_dispersion</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="105" 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">
105
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<td class="diff-line-num new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"kappa"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_DOUBLE</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">kappa</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="106" 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">
106
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<td class="diff-line-num new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"label_uncorrected_tree"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_STRING</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">label_original_tree</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="107" 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="109" 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">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">add_item</span><span class="p">(</span><span class="s" style="color: #d14;">"output_filtered"</span><span class="p">,</span> <span class="n" style="color: #333;">TP_STRING</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">output_filtered</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="107" 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">
107
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<td class="diff-line-num new_line" data-linenumber="110" 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">
110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="n" style="color: #333;">arg</span><span class="p">.</span><span class="n" style="color: #333;">read_input</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="n" style="color: #333;">argv</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="108" 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">
108
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<td class="diff-line-num new_line" data-linenumber="111" 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">
111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">FASTA_FILE_LIST</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">fasta_file_list</span><span class="p">,</span> <span class="s" style="color: #d14;">"fasta_file_list"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="109" 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">
109
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<td class="diff-line-num new_line" data-linenumber="112" 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">
112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">XMFA_FILE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">xmfa_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"xmfa_file"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="113" 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="116" 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">@@ -113,11 +116,11 @@ int main (const int argc, const char* argv[]) {</td>
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<td class="diff-line-num old_line" data-linenumber="113" 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">
113
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<td class="diff-line-num new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">USE_INCOMPATIBLE_SITES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">use_incompatible_sites</span><span class="p">,</span> <span class="s" style="color: #d14;">"use_incompatible_sites"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="114" 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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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">RESCALE_NO_RECOMBINATION</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">rescale_no_recombination</span><span class="p">,</span> <span class="s" style="color: #d14;">"rescale_no_recombination"</span><span class="p">);</span></span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">SHOW_PROGRESS</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">show_progress</span><span class="p">,</span> <span class="s" style="color: #d14;">"show_progress"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">COMPRESS_RECONSTRUCTED_SITES</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">compress_reconstructed_sites</span><span class="p">,</span> <span class="s" style="color: #d14;">"compress_reconstructed_sites"</span><span class="p">);</span></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">GUESS_INITIAL_M</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">guess_initial_m</span><span class="p">,</span> <span class="s" style="color: #d14;">"guess_initial_m"</span><span class="p">);</span></span>
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">EM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">em</span><span class="p">,</span> <span class="s" style="color: #d14;">"em"</span><span class="p">);</span></span>
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119
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">EMBRANCH</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">embranch</span><span class="p">,</span> <span class="s" style="color: #d14;">"embranch"</span><span class="p">);</span></span>
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120
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">LABEL_ORIGINAL_TREE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">label_original_tree</span><span class="p">,</span> <span class="s" style="color: #d14;">"label_uncorrected_tree"</span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">OUTPUT_FILTERED</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string_to_bool</span><span class="p">(</span><span class="n" style="color: #333;">output_filtered</span><span class="p">,</span> <span class="s" style="color: #d14;">"output_filtered"</span><span class="p">);</span></span>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">MULTITHREAD</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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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">brent_tolerance</span><span class="o" style="font-weight: 600;"><=</span><span class="mf" style="color: #099;">0.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">brent_tolerance</span><span class="o" style="font-weight: 600;">>=</span><span class="mf" style="color: #099;">0.1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="328" 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="331" 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">@@ -328,7 +331,6 @@ int main (const int argc, const char* argv[]) {</td>
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Report the ML</span></span>
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329
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<pre style="margin: 0;"> <span id="LC332" 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;">"Maximum log-likelihood for imputation and ancestral state reconstruction = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">ML</span><span class="p">.</span><span class="n" style="color: #333;">LOG</span><span class="p">()</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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330
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="cpp"> </span>
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331
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<pre style="margin: 0;">-<span id="LC331" 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;">COMPRESS_RECONSTRUCTED_SITES</span><span class="p">)</span> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"WARNING: -compress_reconstructed_sites=false not yet implemented, ignoring."</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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332
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the ML reconstructed sequences</span></span>
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333
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="cpp"> <span class="n" style="color: #333;">write_ancestral_fasta</span><span class="p">(</span><span class="n" style="color: #333;">node_nuc</span><span class="p">,</span> <span class="n" style="color: #333;">ctree_node_labels</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_out_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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334
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336
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// For every position in the original FASTA file, output the corresponding position in the output FASTA file, or -1 (not included)</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">@@ -466,6 +468,11 @@ int main (const int argc, const char* argv[]) {</td>
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466
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the importation status</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp"> <span class="n" style="color: #333;">write_importation_status_intervals</span><span class="p">(</span><span class="n" style="color: #333;">is_imported</span><span class="p">,</span><span class="n" style="color: #333;">ctree_node_labels</span><span class="p">,</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span><span class="n" style="color: #333;">compat</span><span class="p">,</span><span class="n" style="color: #333;">import_out_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="n" style="color: #333;">root_node</span><span class="p">,</span><span class="n" style="color: #333;">chr_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC470" 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;">"Wrote inferred importation status to "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">import_out_file</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="LC471" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">OUTPUT_FILTERED</span><span class="p">)</span> <span class="p">{</span> </span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the filtered alignment</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filtered_fasta</span><span class="p">(</span><span class="n" style="color: #333;">is_imported</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fa</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_site</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_filtered_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC474" 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;">"Wrote filtered alignment to "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">fasta_filtered_file</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="LC475" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If required, simulate under the point estimates and output posterior samples of the parameters</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">emsim</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 unfold js-unfold old_line" data-linenumber="548" 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">@@ -548,6 +555,11 @@ int main (const int argc, const char* argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the importation status</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">write_importation_status_intervals</span><span class="p">(</span><span class="n" style="color: #333;">is_imported</span><span class="p">,</span><span class="n" style="color: #333;">ctree_node_labels</span><span class="p">,</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span><span class="n" style="color: #333;">compat</span><span class="p">,</span><span class="n" style="color: #333;">import_out_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="n" style="color: #333;">root_node</span><span class="p">,</span><span class="n" style="color: #333;">chr_name</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC557" 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;">"Wrote inferred importation status to "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">import_out_file</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="LC558" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">OUTPUT_FILTERED</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Output the filtered alignment</span></span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">write_filtered_fasta</span><span class="p">(</span><span class="n" style="color: #333;">is_imported</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fa</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_site</span><span class="p">,</span> <span class="n" style="color: #333;">fasta_filtered_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">+<span id="LC561" 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;">"Wrote filtered alignment to "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">fasta_filtered_file</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="LC562" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="cpp"> </span>
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564
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If required, simulate under the point estimates and output posterior samples of the parameters</span></span>
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">emsim</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1721,17 +1733,7 @@ void write_ancestral_fasta(Matrix<Nucleotide> &nuc, vector<string> &all_node_nam</td>
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1721
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1733
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<pre style="margin: 0;"> <span id="LC1733" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_ancestral_fasta(): could not open file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for writing"</span><span class="p">;</span></span>
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1722
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1734
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<pre style="margin: 0;"> <span id="LC1734" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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1723
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1735
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<pre style="margin: 0;"> <span id="LC1735" class="line" lang="cpp"> <span class="p">}</span></span>
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1724
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<pre style="margin: 0;">-<span id="LC1724" class="line" lang="cpp"> <span class="n" style="color: #333;">write_ancestral_fasta</span><span class="p">(</span><span class="n" style="color: #333;">nuc</span><span class="p">,</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span><span class="n" style="color: #333;">fout</span><span class="p">);</span></span>
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1725
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<pre style="margin: 0;">-<span id="LC1725" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1726
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<pre style="margin: 0;">-<span id="LC1726" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1727" class="line" lang="cpp"></span>
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1728
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<pre style="margin: 0;">-<span id="LC1728" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_ancestral_fasta</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Nucleotide</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nuc</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1729" 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">
1729
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1736
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<pre style="margin: 0;"> <span id="LC1736" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">AGCTN</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="sc" style="color: #d14;">'A'</span><span class="p">,</span><span class="sc" style="color: #d14;">'G'</span><span class="p">,</span><span class="sc" style="color: #d14;">'C'</span><span class="p">,</span><span class="sc" style="color: #d14;">'T'</span><span class="p">,</span><span class="sc" style="color: #d14;">'N'</span><span class="p">};</span></span>
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1730
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<pre style="margin: 0;">-<span id="LC1730" 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;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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1731
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<pre style="margin: 0;">-<span id="LC1731" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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1732
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<td class="diff-line-num new_line old" data-linenumber="1737" 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="LC1732" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_ancestral_fasta(): could not open file stream for writing"</span><span class="p">;</span></span>
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1733
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<pre style="margin: 0;">-<span id="LC1733" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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1734
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<pre style="margin: 0;">-<span id="LC1734" class="line" lang="cpp"> <span class="p">}</span></span>
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1735
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1737
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<pre style="margin: 0;"> <span id="LC1737" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nuc</span><span class="p">.</span><span class="n" style="color: #333;">nrows</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">all_node_names</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="p">{</span></span>
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1736
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1738
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<pre style="margin: 0;"> <span id="LC1738" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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1737
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<td class="diff-line-num new_line" data-linenumber="1739" 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">
1739
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<pre style="margin: 0;"> <span id="LC1739" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_ancestral_fasta(): number of sequences ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">nuc</span><span class="p">.</span><span class="n" style="color: #333;">nrows</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") does not equal number of node labels ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">all_node_names</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</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="1745" 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="1747" 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">@@ -1745,23 +1747,37 @@ void write_ancestral_fasta(Matrix<Nucleotide> &nuc, vector<string> &all_node_nam</td>
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<pre style="margin: 0;"> <span id="LC1747" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</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="LC1749" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;">+<span id="LC1750" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1751" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1752" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1750" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_<span class="idiff left">position_cross_reference</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">iscompat</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">ipat</span></span><span class="p">,</span> <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;">file_name</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1753" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_<span class="idiff left">filtered_fasta</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></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">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">ImportationState</span></span><span class="o" style="font-weight: 600;"><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="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">imported</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DNA</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">fa</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">ignore_site</span></span><span class="p">,</span> <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;">file_name</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1754" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC1755" 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;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1756" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1754" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_<span class="idiff left right">position_cross_reference</span>(): could not open file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for writing"</span><span class="p">;</span></span>
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1757
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<pre style="margin: 0;">+<span id="LC1757" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_<span class="idiff left right">filtered_fasta</span>(): could not open file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for writing"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1758" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC1759" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1757" class="line" lang="cpp"> <span class="n" style="color: #333;">write_position_cross_reference</span><span class="p">(</span><span class="n" style="color: #333;">iscompat</span><span class="p">,</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span><span class="n" style="color: #333;">fout</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1758" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1760
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<pre style="margin: 0;">+<span id="LC1760" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1761" 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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tokeep</span><span class="p">(</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lseq</span><span class="p">);</span></span>
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1762
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<pre style="margin: 0;">+<span id="LC1762" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lseq</span><span class="p">;</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1763" 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">
1763
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<pre style="margin: 0;">+<span id="LC1763" class="line" lang="cpp"> <span class="n" style="color: #333;">tokeep</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</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 new new_line" data-linenumber="1764" 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">
1764
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<pre style="margin: 0;">+<span id="LC1764" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">ignore_site</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">])</span> <span class="n" style="color: #333;">tokeep</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</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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<td class="diff-line-num new new_line" data-linenumber="1765" 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">
1765
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<pre style="margin: 0;">+<span id="LC1765" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">n</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;">n</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">imported</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">imported</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">]</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">Imported</span><span class="p">)</span> <span class="n" style="color: #333;">tokeep</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">]</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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<td class="diff-line-num new new_line" data-linenumber="1766" 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">
1766
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<pre style="margin: 0;">+<span id="LC1766" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1767" 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">
1767
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<pre style="margin: 0;">+<span id="LC1767" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">n</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;">n</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">nseq</span><span class="p">;</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1768" 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">
1768
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<pre style="margin: 0;">+<span id="LC1768" class="line" lang="cpp"> <span class="p">{</span></span>
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1769
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<pre style="margin: 0;">+<span id="LC1769" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">label</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">]</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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1770
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<pre style="margin: 0;">+<span id="LC1770" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">lseq</span><span class="p">;</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1771" 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">
1771
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<pre style="margin: 0;">+<span id="LC1771" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tokeep</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">])</span> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">fa</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="n" style="color: #333;">n</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1772" 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">
1772
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<pre style="margin: 0;">+<span id="LC1772" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</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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1773
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<pre style="margin: 0;">+<span id="LC1773" class="line" lang="cpp"> <span class="p">}</span> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1759
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1774
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<pre style="margin: 0;"> <span id="LC1774" class="line" lang="cpp"><span class="p">}</span></span>
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1760
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1775
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<pre style="margin: 0;"> <span id="LC1775" class="line" lang="cpp"></span>
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1761
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<td class="diff-line-num new_line old" data-linenumber="1776" 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="LC1761" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_position_cross_reference</span><span class="p">(</span><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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">iscompat</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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1776
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<pre style="margin: 0;">+<span id="LC1776" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_position_cross_reference</span><span class="p">(</span><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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">iscompat</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span> <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;">file_name</span><span class="p">)</span> <span class="p">{</span></span>
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1777
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<pre style="margin: 0;">+<span id="LC1777" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>
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1762
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1778
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<pre style="margin: 0;"> <span id="LC1778" 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;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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1763
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1779
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<pre style="margin: 0;"> <span id="LC1779" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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1764
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<td class="diff-line-num new_line old" data-linenumber="1780" 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="LC1764" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_position_cross_reference(): could not open file <span class="idiff left right">stream</span> for writing"</span><span class="p">;</span></span>
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1780
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<pre style="margin: 0;">+<span id="LC1780" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_position_cross_reference(): could not open file <span class="idiff left">"</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">file_name</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"</span> for writing"</span><span class="p">;</span></span>
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1765
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1781
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<pre style="margin: 0;"> <span id="LC1781" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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1766
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1782
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<pre style="margin: 0;"> <span id="LC1782" class="line" lang="cpp"> <span class="p">}</span></span>
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1767
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1783
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<pre style="margin: 0;"> <span id="LC1783" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">j</span><span class="p">,</span><span class="n" style="color: #333;">pat</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1780" 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="1796" 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">@@ -1780,6 +1796,7 @@ void write_position_cross_reference(vector<bool> &iscompat, vector<int> &ipat, o</td>
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1780
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1796
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<pre style="margin: 0;"> <span id="LC1796" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pat</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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1781
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1797
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<pre style="margin: 0;"> <span id="LC1797" class="line" lang="cpp"> <span class="p">}</span></span>
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1782
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1798
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<pre style="margin: 0;"> <span id="LC1798" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</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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1799
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<pre style="margin: 0;">+<span id="LC1799" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1783
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1800
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<pre style="margin: 0;"> <span id="LC1800" class="line" lang="cpp"><span class="p">}</span></span>
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1784
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1801
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<pre style="margin: 0;"> <span id="LC1801" class="line" lang="cpp"></span>
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1785
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1802
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<pre style="margin: 0;"> <span id="LC1802" class="line" lang="cpp"><span class="n" style="color: #333;">mydouble</span> <span class="nf" style="color: #900; font-weight: 600;">likelihood_branch</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dec_id</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">anc_id</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Nucleotide</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node_nuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pat1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cpat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">kappa</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pinuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">branch_length</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1810" 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="1827" 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">@@ -1810,55 +1827,6 @@ bool string_to_bool(const string s, const string label) {</td>
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1810
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1827
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<pre style="margin: 0;"> <span id="LC1827" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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1811
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1828
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<pre style="margin: 0;"> <span id="LC1828" class="line" lang="cpp"><span class="p">}</span></span>
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1812
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1829
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<pre style="margin: 0;"> <span id="LC1829" class="line" lang="cpp"></span>
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1813
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<pre style="margin: 0;">-<span id="LC1813" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <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;">file_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1814" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC1815" 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;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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1816
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<pre style="margin: 0;">-<span id="LC1816" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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1817
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1817" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_importation_status(): could not open file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for writing"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1818" 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">
1818
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<pre style="margin: 0;">-<span id="LC1818" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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1819
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<pre style="margin: 0;">-<span id="LC1819" class="line" lang="cpp"> <span class="p">}</span></span>
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1820
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<pre style="margin: 0;">-<span id="LC1820" class="line" lang="cpp"> <span class="n" style="color: #333;">write_importation_status</span><span class="p">(</span><span class="n" style="color: #333;">imported</span><span class="p">,</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span><span class="n" style="color: #333;">compat</span><span class="p">,</span><span class="n" style="color: #333;">fout</span><span class="p">,</span><span class="n" style="color: #333;">root_node</span><span class="p">);</span></span>
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1821
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<pre style="margin: 0;">-<span id="LC1821" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1822
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<pre style="margin: 0;">-<span id="LC1822" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1823" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1824" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1825" 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;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1826" 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">
1826
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<pre style="margin: 0;">-<span id="LC1826" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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1827
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<pre style="margin: 0;">-<span id="LC1827" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_importation_status(): could not open file stream for writing"</span><span class="p">;</span></span>
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1828
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<pre style="margin: 0;">-<span id="LC1828" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</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 old_line" data-linenumber="1829" 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">
1829
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<pre style="margin: 0;">-<span id="LC1829" class="line" lang="cpp"> <span class="p">}</span></span>
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1830
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<pre style="margin: 0;">-<span id="LC1830" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">imported</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">root_node</span><span class="p">)</span> <span class="p">{</span></span>
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1831
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<pre style="margin: 0;">-<span id="LC1831" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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1832
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<pre style="margin: 0;">-<span id="LC1832" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_importation_status(): number of lineages ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">imported</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") does not equal the number of non-root node labels ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">root_node</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">")"</span><span class="p">;</span></span>
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1833
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<pre style="margin: 0;">-<span id="LC1833" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</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 old_line" data-linenumber="1834" 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">
1834
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<pre style="margin: 0;">-<span id="LC1834" class="line" lang="cpp"> <span class="p">}</span></span>
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1835
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<pre style="margin: 0;">-<span id="LC1835" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">all_node_names</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">root_node</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1836" 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">
1836
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1836" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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1837
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1837" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_importation_status(): number of non-root lineages ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">root_node</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") exceeds the number of node labels ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">all_node_names</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">")"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1838" 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">
1838
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<pre style="margin: 0;">-<span id="LC1838" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</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 old_line" data-linenumber="1839" 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">
1839
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1839" class="line" lang="cpp"> <span class="p">}</span></span>
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1840
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<pre style="margin: 0;">-<span id="LC1840" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1841" 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">
1841
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<pre style="margin: 0;">-<span id="LC1841" class="line" lang="cpp"> <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;">root_node</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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<td class="diff-line-num old old_line" data-linenumber="1842" 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">
1842
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<pre style="margin: 0;">-<span id="LC1842" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">all_node_names</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;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1843" 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">
1843
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<pre style="margin: 0;">-<span id="LC1843" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</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="p">;</span></span>
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1844
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<pre style="margin: 0;">-<span id="LC1844" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="n" style="color: #333;">pos</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;">pos</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">isBLC</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1845" 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">
1845
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1845" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">isBLC</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">])</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1846" 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">
1846
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1846" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If used in branch length correction, 0 (unimported), 1 (imported), 2 (homoplasy/multiallelic unimported), 3 (homoplasy/multiallelic imported)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1847" 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">
1847
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1847" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">compat</span><span class="p">[</span><span class="n" style="color: #333;">pos</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="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">imported</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">k</span><span class="p">];</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1848" 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">
1848
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1848" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</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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<td class="diff-line-num old old_line" data-linenumber="1849" 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">
1849
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<td class="diff-line-num new_line old" data-linenumber="1830" 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="LC1849" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">k</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1850" 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">
1850
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<pre style="margin: 0;">-<span id="LC1850" class="line" lang="cpp"> <span class="p">}</span> <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;">compat</span><span class="p">[</span><span class="n" style="color: #333;">pos</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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<pre style="margin: 0;">-<span id="LC1851" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If compatible but not used in branch length correction, 4</span></span>
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<pre style="margin: 0;">-<span id="LC1852" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1853" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1854" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If homoplasy/multiallelic and not used in branch length correction, 5</span></span>
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<pre style="margin: 0;">-<span id="LC1855" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1856" class="line" lang="cpp"> <span class="p">}</span></span>
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1857
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<pre style="margin: 0;">-<span id="LC1857" class="line" lang="cpp"> <span class="p">}</span></span>
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1858
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<pre style="margin: 0;">-<span id="LC1858" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</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="LC1859" class="line" lang="cpp"> <span class="p">}</span> </span>
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<pre style="margin: 0;">-<span id="LC1860" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1861" class="line" lang="cpp"></span>
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1830
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<pre style="margin: 0;"> <span id="LC1830" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status_intervals</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <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;">file_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">,</span> <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;">chr_name</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1831" class="line" lang="cpp"> <span class="n" style="color: #333;">ofstream</span> <span class="n" style="color: #333;">fout</span><span class="p">(</span><span class="n" style="color: #333;">file_name</span><span class="p">);</span></span>
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1832
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<pre style="margin: 0;"> <span id="LC1832" 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;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1866" 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="1834" 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">@@ -1866,16 +1834,6 @@ void write_importation_status_intervals(vector< vector<ImportationState> > &impo</td>
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1866
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1834
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<pre style="margin: 0;"> <span id="LC1834" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_importation_status_intervals(): could not open file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">file_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" for writing"</span><span class="p">;</span></span>
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1867
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1835
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<pre style="margin: 0;"> <span id="LC1835" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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1868
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1836
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<pre style="margin: 0;"> <span id="LC1836" class="line" lang="cpp"> <span class="p">}</span></span>
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1869
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<td class="diff-line-num new_line old" data-linenumber="1837" 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="LC1869" class="line" lang="cpp"> <span class="n" style="color: #333;">write_importation_status_intervals</span><span class="p">(</span><span class="n" style="color: #333;">imported</span><span class="p">,</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span><span class="n" style="color: #333;">compat</span><span class="p">,</span><span class="n" style="color: #333;">fout</span><span class="p">,</span><span class="n" style="color: #333;">root_node</span><span class="p">,</span> <span class="n" style="color: #333;">chr_name</span><span class="p">);</span></span>
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1870
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<pre style="margin: 0;">-<span id="LC1870" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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1871
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<pre style="margin: 0;">-<span id="LC1871" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC1872" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1873" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status_intervals</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">,</span> <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;">chr_name</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1874" 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;">fout</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC1875" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1876" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_importation_status_intervals(): could not open file stream for writing"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC1877" class="line" lang="cpp"> <span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">errTxt</span><span class="p">.</span><span class="n" style="color: #333;">str</span><span class="p">().</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC1878" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1837" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">imported</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">root_node</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC1838" class="line" lang="cpp"> <span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">errTxt</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1839" class="line" lang="cpp"> <span class="n" style="color: #333;">errTxt</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"write_importation_status_intervals(): number of lineages ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">imported</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">") does not equal the number of non-root node labels ("</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">root_node</span> <span class="o" style="font-weight: 600;"><<</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="1916" 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">@@ -1916,6 +1874,7 @@ void write_importation_status_intervals(vector< vector<ImportationState> > &impo</td>
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<pre style="margin: 0;"> <span id="LC1874" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">fout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">chr_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">interval_beg</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">all_node_names</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;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC1875" class="line" lang="cpp"> <span class="p">}</span></span>
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1876
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<pre style="margin: 0;"> <span id="LC1876" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1877" class="line" lang="cpp"> <span class="n" style="color: #333;">fout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC1878" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1879" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1880" class="line" lang="cpp"><span class="n" style="color: #333;">mydouble</span> <span class="nf" style="color: #900; font-weight: 600;">maximum_likelihood_ClonalFrame_branch_allsites</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dec_id</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">anc_id</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Nucleotide</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node_nuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">iscompat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">kappa</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pinuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">branch_length</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rho_over_theta</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mean_import_length</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">import_divergence</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;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">is_imported</span><span class="p">)</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#35e88b2c83f4a27277510a3997b027f1a9bd2c74"><strong>src/main.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* Copyright 2013 Daniel Wilson and Xavier Didelot.</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* </span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * main.h</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part of ClonalFrameML</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</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">@@ -22,23 +21,20 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string.h></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils/newick.h"</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include "coalesce/coalesce.h"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "coalesce/coalescent_record.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include "myutils/myutils.h"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "xmfa.h"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils/DNA.h"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils/mydouble.h"</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include "coalesce/mutation.h"</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "powell.h"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils/argumentwizard.h"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils/random.h"</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iomanip></span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#<span class="idiff left right">include "version.h</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#<span class="idiff left right">define ClonalFrameML_version "v1.12</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">cout</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">myutils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">NewickTree</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">@@ -68,15 +64,12 @@ void write_newick(const marginal_tree &ctree, const vector<string> &all_node_nam</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_newick</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">marginal_tree</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ctree</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_newick_node</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">mt_node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_ancestral_fasta</span><span class="p">(</span><span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Nucleotide</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">nuc</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">file_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_<span class="idiff left">ancestral_fasta</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Matrix</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">Nucleotide</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">nuc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">all_node_names</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ofstream</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff right">fout</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_<span class="idiff left">filtered_fasta</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></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">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">ImportationState</span></span><span class="o" style="font-weight: 600;"><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="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="n" style="color: #333;"><span class="idiff">imported</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">DNA</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">fa</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">vector</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">bool</span></span><span class="o" style="font-weight: 600;"><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">ignore_site</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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 right">file_name</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_position_cross_reference</span><span class="p">(</span><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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">iscompat</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span> <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;">file_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_position_cross_reference</span><span class="p">(</span><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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">iscompat</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"><span class="n" style="color: #333;">mydouble</span> <span class="nf" style="color: #900; font-weight: 600;">likelihood_branch</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">dec_id</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">anc_id</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Nucleotide</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node_nuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pat1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cpat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">kappa</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pinuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">branch_length</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="nf" style="color: #900; font-weight: 600;">string_to_bool</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">label</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <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;">file_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status_intervals</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <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;">file_name</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">,</span><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;">chr_name</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">write_importation_status_intervals</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;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">ImportationState</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">imported</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;">string</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">all_node_names</span><span class="p">,</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">isBLC</span><span class="p">,</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">compat</span><span class="p">,</span> <span class="n" style="color: #333;">ofstream</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fout</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">root_node</span><span class="p">,</span> <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;">chr_name</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">Baum_Welch</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">marginal_tree</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Nucleotide</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node_nuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">kappa</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pinuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">informative</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prior_a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prior_b</span><span class="p">,</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">full_param</span><span class="p">,</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">posterior_a</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">neval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">coutput</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;">priorL</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">Baum_Welch0</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">marginal_tree</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Matrix</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Nucleotide</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">node_nuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">position</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">int</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ipat</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">kappa</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pinuc</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">informative</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prior_a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">prior_b</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">full_param</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">posterior_a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">coutput</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="nf" style="color: #900; font-weight: 600;">gamma_loglikelihood</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#de95940302a3683bcc91f922486d23809965fa7b"><strong>src/make.sh</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"#define ClonalFrameML_GITRevision </span><span class="se" style="color: #d14;">\"</span><span class="sb" style="color: #d14;">`</span>git describe <span class="nt" style="color: #000080;">--tags</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span> version.h</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell">g++ main.cpp <span class="nt" style="color: #000080;">-o</span> ClonalFrameML <span class="nt" style="color: #000080;">-I</span> ./ <span class="nt" style="color: #000080;">-I</span> ./myutils <span class="nt" style="color: #000080;">-I</span> ./coalesce <span class="nt" style="color: #000080;">-O3</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell">g++ main.cpp <span class="nt" style="color: #000080;">-o</span> ClonalFrameML <span class="nt" style="color: #000080;">-O3</span></span></pre>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#cf908ec768cf4b8af024fa45c591d82366d8b622"><strong>src/make_win.bat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="batchfile">@echo <span class="na" style="color: #008080;">off</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="batchfile"><span class="c" style="color: #998; font-style: italic;">rem This creates the version.h file. </span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="batchfile"><span class="c" style="color: #998; font-style: italic;">rem You need git installed (obviously)</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="batchfile"><span class="c" style="color: #998; font-style: italic;">rem And to be in the folder where the ".git" directory exists.</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="batchfile"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="batchfile"><span class="kd" style="font-weight: 600;">FOR</span> <span class="na" style="color: #008080;">/F </span><span class="s2" style="color: #d14;">"delims="</span> <span class="vm">%%i</span> <span class="kd" style="font-weight: 600;">IN</span> <span class="o" style="font-weight: 600;">(</span><span class="s1" style="color: #d14;">'git describe --tags'</span><span class="o" style="font-weight: 600;">)</span> <span class="kd" style="font-weight: 600;">DO</span> <span class="kd" style="font-weight: 600;">set</span> <span class="kd" style="font-weight: 600;">GITRESULT</span><span class="o" style="font-weight: 600;">=</span><span class="vm">%%i</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="batchfile"><span class="nb" style="color: #0086b3;">echo</span> #define <span class="kd" style="font-weight: 600;">ClonalFrameML_GITRevision</span> <span class="nv" style="color: #008080;">%GITRESULT%</span> <span class="o" style="font-weight: 600;">></span> <span class="kd" style="font-weight: 600;">version</span>.h</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="batchfile"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="batchfile"><span class="c" style="color: #998; font-style: italic;">rem The linux make.sh file now compiles the code.</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="batchfile"><span class="c" style="color: #998; font-style: italic;">rem If you're in VS, remember you need _CRT_SECURE_NO_WARNINGS in the</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="batchfile"><span class="c" style="color: #998; font-style: italic;">rem Pre-Processor code.</span></span></pre>
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<li id="58ea1bfb97fa00a98b822ca930a2003aafdcc2b2">
<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#58ea1bfb97fa00a98b822ca930a2003aafdcc2b2"><strong>src/makefile</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Make<span class="idiff left right"> </span>file for ClonalFrameML</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Makefile for ClonalFrameML</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: #008080;">CC</span> <span class="o" style="font-weight: 600;">=</span> g++</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;">-O3</span> <span class="nt" style="color: #000080;">-I</span>./ <span class="nt" style="color: #000080;">-I</span>./myutils <span class="nt" style="color: #000080;">-I</span>./coalesce</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">=</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;">-O3</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: #008080;">OBJECTS</span> <span class="o" style="font-weight: 600;">=</span> main.o</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">HEADERS</span> <span class="o" style="font-weight: 600;">=</span> main.h brent.h powell.h<span class="idiff left right"> version.h</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">HEADERS</span> <span class="o" style="font-weight: 600;">=</span> main.h brent.h powell.h</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean <span class="idiff left right">version</span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean </span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">version </span>ClonalFrameML</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">ClonalFrameML</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nl">ClonalFrameML</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">$(OBJECTS)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(LDFLAGS)</span> <span class="nt" style="color: #000080;">-o</span> ClonalFrameML <span class="nv" style="color: #008080;">$(OBJECTS)</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">@@ -15,8 +14,5 @@ ClonalFrameML: $(OBJECTS)</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"><span class="nl">main.o</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">main.cpp $(HEADERS)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="make"> <span class="nv" style="color: #008080;">$(CC)</span> <span class="nv" style="color: #008080;">$(CFLAGS)</span> <span class="nt" style="color: #000080;">-c</span> <span class="nt" style="color: #000080;">-o</span> main.o main.cpp</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="make"><span class="nl">version</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="make"> /bin/echo <span class="s2" style="color: #d14;">"#define ClonalFrameML_GITRevision </span><span class="se" style="color: #d14;">\"</span><span class="sb" style="color: #d14;">`</span>git describe <span class="nt" style="color: #000080;">--tags</span><span class="sb" style="color: #d14;">`</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span> version.h</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nl">clean</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nv" style="color: #008080;">$(OBJECTS)</span></span></pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="make"> <span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;"><span class="idiff left">-f</span></span><span class="idiff right"> </span><span class="nv" style="color: #008080;">$(OBJECTS)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#c55b64645d65c9e2a27db3d7565770bde31f9da2"><strong>src/myutils/DNA.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">@@ -31,7 +31,7 @@</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <string></span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <fstream></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils<span class="idiff left right">/myutils</span>.h"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils.h"</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <map></span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <algorithm></span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#cd26defada1861c5b038b653e115f3bdcaaed57f"><strong>src/myutils/argumentwizard.h</strong></a>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <ctype.h></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "my<span class="idiff left right">utils/my</span>error.h"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myerror.h"</span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">myutils</span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#da4d8eb3d85cdb96ef65c02bd1c1f72abc11be13"><strong>src/myutils/matrix.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">@@ -27,8 +27,8 @@</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "<span class="idiff left right">myutils/</span>vector.h"</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "<span class="idiff left right">myutils/</span>utils.h"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "vector.h"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "utils.h"</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/****************************************************************/</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* myutils::Matrix */</span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#babfe00df23f6a3872b2a45917e09a3a816f760e"><strong>src/myutils/mydouble.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">@@ -21,7 +21,7 @@</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <math.h></span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "my<span class="idiff left right">utils/my</span>error.h"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myerror.h"</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="n" style="color: #333;">myutils</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">error</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#7f8f3fa1108c142e7dca8a7e12a0748266721009"><strong>src/myutils/myutils.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">@@ -27,26 +27,12 @@</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#pragma warning(disable: 4786)</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="c"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*Includes all header files in the myutils directory*/</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/*#include "cmatrix.h"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "myerror.h"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "utils.h"</span></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 "vector.h"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "matrix.h"</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;">#include "lotri_matrix.h"</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "random.h"</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">#include "error.h"</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "DNA.h"</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">#include "vector.h"*/</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="c"></span>
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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 "myutils/myerror.h"</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils/utils.h"</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//#include "myutils/cmatrix.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 "myutils/vector.h"</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "myutils/matrix.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 "myutils/lotri_matrix.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 "myutils/random.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 "myutils/DNA.h"</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//#include "myutils/pause.h"</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//#include "myutils/sort.h"</span></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="c1" style="color: #998; font-style: italic;">//#include "controlwizard.h" /* has problems in Linux with pointers */</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//#include "pause.h" /* removed because conio.h is not standard */</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC38" 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/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#f12fd2aa978269f84dbda0eae3876a5abbf73e53"><strong>src/myutils/newick.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">@@ -10,7 +10,7 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define _NEWICK_H_</span></span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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12
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12
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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 <string></span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "my<span class="idiff left right">utils/my</span>error.h"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myerror.h"</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <sstream></span></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#3e5424c84a4c10d54b1c282c29d136c829599c14"><strong>src/myutils/random.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">@@ -28,11 +28,11 @@</td>
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cmath></span></span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <time.h></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "<span class="idiff left right">myutils/</span>vector.h"</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "m<span class="idiff left right">yutils/m</span>atrix.h"</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "<span class="idiff left right">myutils/</span>lotri_matrix.h"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "vector.h"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "matrix.h"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "lotri_matrix.h"</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "my<span class="idiff left right">utils/my</span>error.h"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myerror.h"</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">myutils</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Random</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#f9da5063f22ad9d93eb62625d4d230ef61a108ed"><strong>src/myutils/vector.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">@@ -25,7 +25,7 @@</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef _MYUTILS_VECTOR_H_</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define _MYUTILS_VECTOR_H_</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "my<span class="idiff left right">utils/my</span>error.h"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "myerror.h"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdlib.h></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <stdio.h></span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//#include <myutils.h></span></span>
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<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#527894afe3e57b9af044db6abe11da84f2e49349"><strong>src/powell.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* Copyright 2013 Daniel Wilson.</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* </span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * powell.h</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Part of ClonalFrameML</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">The myutils library</span> is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">ClonalFrameML</span> is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU Lesser General Public License as published by</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * (at your option) any later version.</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">The myutils library</span> is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * <span class="idiff left right">ClonalFrameML</span> is distributed in the hope that it will be useful,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * GNU Lesser General Public License for more details.</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * </span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * You should have received a copy of the GNU Lesser General Public License</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * along with <span class="idiff left right">the myutils library</span>. If not, see <http://www.gnu.org/licenses/>.</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * along with <span class="idiff left right">ClonalFrameML</span>. If not, see <http://www.gnu.org/licenses/>.</span></span>
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17
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Parts of this code are based on code in Numerical Recipes in C++</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * WH Press, SA Teukolsky, WT Vetterling, BP Flannery (2002).</span></span>
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<li id="6c2ab301f53181757580a150882c67375310825f">
<a href="https://salsa.debian.org/med-team/clonalframeml/-/commit/81343d66151bae0c5c45fca53761c4eab15bbb16#6c2ab301f53181757580a150882c67375310825f"><strong>src/xmfa.h</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Copyright 2013 Daniel Wilson and Xavier Didelot.</span></span>
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<pre style="margin: 0;">-<span id="LC2" 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="LC1" 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="LC2" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * xmfa.h</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * Part of ClonalFrameML</span></span>
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<pre style="margin: 0;"> <span id="LC4" 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="LC5" 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="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * ClonalFrameML is free software: you can redistribute it and/or modify</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * it under the terms of the GNU Lesser General Public License as published by</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> * the Free Software Foundation, either version 3 of the License, or</span></span>
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