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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/sweed">Debian Med / sweed</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sweed/commit/35a62195f37354893d2d117b0c9f5233981e1dd2">35a62195</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T09:35:28+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.2.1+dfsg</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#fda3484edf8db0684440157ce0b110d784d42704">
README.txt
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<li class="file-stats">
<a href="#14cd7590257a6b3221b1f6928c5f2c5c31097766">
<span class="deleted-file">
−
SweeD.h~
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<h4>Changes:</h4>
<li id="fda3484edf8db0684440157ce0b110d784d42704">
<a href="https://salsa.debian.org/med-team/sweed/commit/35a62195f37354893d2d117b0c9f5233981e1dd2#fda3484edf8db0684440157ce0b110d784d42704"><strong>README.txt</strong></a>
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<li id="14cd7590257a6b3221b1f6928c5f2c5c31097766">
<a href="https://salsa.debian.org/med-team/sweed/commit/35a62195f37354893d2d117b0c9f5233981e1dd2#14cd7590257a6b3221b1f6928c5f2c5c31097766"><strong>SweeD.h~</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">/* </span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> * SweeD</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"> * Copyright September 2012 by Nikolaos Alachiotis and Pavlos Pavlidis</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"> * This program is free software; you may redistribute it and/or modify its</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * under the terms of the GNU General Public License as published by the Free</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * Software Foundation; either version 2 of the License, or (at your option)</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> * any later version.</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"> * This program is distributed in the hope that it will be useful, but</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> * for more details.</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> *</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> * For any other enquiries send an email to</span>
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<td class="diff-line-num old old_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext"> * Pavlos Pavlidis (pavlidisp@gmail.com) or</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> * Nikolaos Alachiotis (n.alachiotis@gmail.com)</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> * </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> */</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">#ifndef _SweeD_H</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#define _SweeD_H</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">#include <stdio.h></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#include <stdlib.h></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">#include <string.h></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">#include <assert.h></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#include <math.h></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">#include <time.h></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">#include <sys/time.h></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">#include <limits.h></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">#include "SweeD_BFGS.h"</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">#ifdef _USE_PTHREADS</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">#include <pthread.h></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">#include <unistd.h></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">#define EXIT 127</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">#define BUSYWAIT 0</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">#define LIKSFS 1</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">#define COMPRVLUT 2</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">#define COMPALPHA 3</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">#ifdef _DO_CHECKPOINTS</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">#include "dmtcpaware.h"</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">#endif</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"></span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">#ifdef _ANALYTICAL_SFS</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">#include <mpfr.h></span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">#include <float.h></span>
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57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">#define ACC 10000</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">#define APPROX 0</span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">#define TOLTIME 1e-7</span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">#define RESCALE 1</span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">#endif</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext"></span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">#define ENTRIES_PER_INT 32</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">#define DENOMINATOR_OFFSET 0.00001</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">#define REGISTER_WIDTH 32</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">#define MAXSIZE 10000</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">#define INFILENAMESIZE 1000</span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">#define SEQNAMESIZE 1000</span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="plaintext">#define DECREASE 0.99</span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="plaintext">#define MINSNPPERWINDOW 5</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="plaintext">#define STRINGLENGTH 100</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">#define VCF_HLENGTH 9 // number of fields in the VCF header line</span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="plaintext">#define MAX_CHROM_NAME_VCF 100</span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">#define MAX_STATES_VCF 5</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext"></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext">#define RESULTS_DEFAULT 0</span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">#define RESULTS_ALL 1</span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext"></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">#define RSQUARE 0</span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">#define DOM 1</span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext">#define ABSDOM 2</span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">#define JUSTD 3</span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">#define ABSD 4</span>
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84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">#define ABSDOM2 5</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">#define ZERO '0'</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="plaintext">#define ONE '1'</span>
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88
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">#define GAP '-'</span>
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89
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="plaintext">#define AD 'A'</span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">#define CY 'C'</span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="plaintext">#define GU 'G'</span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">#define TH 'T'</span>
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93
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">#define UN 'N'</span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext"></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">#define BINARY 2</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">#define BINARY_WITH_GAPS 3</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">#define DNA 4</span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">#define DNA_WITH_GAPS 5</span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">#define STATESALL 8</span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="plaintext"></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="plaintext">#define OTHER_FORMAT -1</span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="plaintext">#define MS_FORMAT 0</span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">#define FASTA_FORMAT 1</span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext">#define MACS_FORMAT 2</span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">#define VCF_FORMAT 3</span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">#define SF_FORMAT 4</span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext"></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext">#define INTOKS 8</span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="plaintext"></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="plaintext">#define N_REF 2</span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="plaintext">#define N_ALT 3</span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">#define N_INFO 6</span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext">#define MAX_STATES 100</span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">#define MAXINT 2147483647</span>
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115
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext"></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">char bits_in_16bits [0x1u << 16];</span>
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118
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="plaintext"></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">int linkage_disequilibrium;</span>
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120
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="plaintext"></span>
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121
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="plaintext">int borderTol;</span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext"></span>
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123
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">int VCF_header_lines;</span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="plaintext">char VCF_alignment_name [MAX_CHROM_NAME_VCF];</span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">int VCF_first_SNP;</span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="plaintext">int nxtVCFalignment;</span>
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127
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="plaintext"></span>
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128
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="plaintext">char runName[INFILENAMESIZE];</span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="plaintext">typedef float cor_t;</span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext"></span>
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132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext"></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext"></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">cor_t ABS (cor_t input);</span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext">double mainTime0;</span>
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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">int map[INTOKS];</span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext"></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext">int nofTokens;</span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="plaintext"></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext">int nofSamples;</span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"></span>
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144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">typedef int al_t;</span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="plaintext">typedef double t_sfs;</span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="plaintext">struct pattern</span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="plaintext">{</span>
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149
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"> int x;</span>
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150
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext"> int n;</span>
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151
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="plaintext"> unsigned char f;</span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"> int c;</span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext"> struct pattern * nxt; </span>
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154
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext">};</span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext">typedef struct </span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="plaintext">{</span>
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158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="plaintext"> al_t *n; // number of valid bases in every site</span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext"> al_t *n_t; // number of valid bases in every site</span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"> al_t *x; // number of derived bases in every site</span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"> al_t *x_t; // number of derived bases in every site</span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext"> float * positions;</span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="plaintext"> int * positionsInd;</span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext"> int * p_t;</span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="plaintext"> unsigned char *folded;</span>
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166
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="plaintext"> unsigned char *f_t;</span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"> unsigned char userSetFolded;</span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext"> unsigned char userSFS;</span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="plaintext"> char* outgroupSequence;</span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext"> char* outgroupName;</span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="plaintext"> int outgroupIndex;</span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="plaintext"> int sequences;</span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="plaintext"> int foldedFormat; // if outgroup exists we set this to zero</span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext"> int segsites; </span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext"> int length;</span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext"></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext"> int minn;</span>
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<td class="diff-line-num old old_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="plaintext"> int minx; </span>
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<td class="diff-line-num old old_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="plaintext"> int maxn;</span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="plaintext"> int maxx;</span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext"> al_t * stateA;</span>
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183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="plaintext"> al_t * stateC;</span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"> al_t * stateG;</span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="plaintext"> al_t * stateT;</span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="plaintext"></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="plaintext"> t_sfs * SFS;</span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext"> t_sfs * tmpSFS;</span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext"> int startSFS;</span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="plaintext"> int endSFS;</span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext"></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="plaintext"> int * ng;</span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext"></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext"> t_sfs * lb;</span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext"> t_sfs * ub;</span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="plaintext"></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext"> int params;</span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="plaintext"></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext"> al_t * n_pat;</span>
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<td class="diff-line-num old old_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="plaintext"> al_t * x_pat;</span>
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<td class="diff-line-num old old_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext"> unsigned char * f_pat;</span>
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<td class="diff-line-num old old_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext"> int * c_pat;</span>
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<td class="diff-line-num old old_line" data-linenumber="204" 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">
204
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="plaintext"> int patterns;</span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="plaintext"></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext"> t_sfs *** gridProbs;</span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext"> t_sfs * gridADs;</span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="plaintext"> t_sfs interval;</span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="plaintext"> t_sfs logAD0; </span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext"></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="plaintext"> t_sfs * baseLikelihood;</span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="plaintext"></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext"> struct pattern * patternList;</span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="plaintext"> float sweepStep;</span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="plaintext"> int discSites;</span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="plaintext">#ifdef _USE_PTHREADS</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext"> t_sfs * threadScoresLIKSFS;</span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext">} alignment_struct;</span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext">alignment_struct * alignment;</span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="plaintext">double * rv;</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="plaintext">double ** rvLUT;</span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="plaintext">double ** rvLUT2;</span>
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230
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext"></span>
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231
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="plaintext">#define GRIDSIZE 300</span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="plaintext">#define LOCALGRIDSIZE 100</span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="plaintext">double div6; </span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="plaintext">typedef struct</span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="plaintext">{</span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="plaintext"> double * val;</span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="plaintext"> int * sc;</span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="plaintext">} factorial_LUT;</span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="plaintext">factorial_LUT * factLUT;</span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="plaintext">typedef struct</span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="plaintext">{</span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="plaintext"> int sfRealPos; </span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="plaintext"> t_sfs likelihood; </span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="plaintext"> t_sfs alpha; </span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="plaintext">} clr_struct;</span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="plaintext">clr_struct * clr;</span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext">#ifdef _ANALYTICAL_SFS</span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="plaintext">typedef struct</span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="plaintext">{</span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="plaintext"> double t;</span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="plaintext"> double d;</span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext">} event;</span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="plaintext"></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="plaintext">int eventsTotal;</span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="plaintext">event * eventList;</span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="plaintext"></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="plaintext">mpfr_t ** analyticalSFS_LUT;</span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext"></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext">void computeAnalyticalSFS(int sequences, FILE * fp);</span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="plaintext">void computeAnalyticalSFSExpo(int sequences, double R, FILE * fpSFSo);</span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="plaintext">long double xExponential_Integral_Ei( long double x );</span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="plaintext">void mpfr_Exponential_Integral_Ei( mpfr_t EImp, mpfr_t xmp );</span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="plaintext"></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="plaintext">void printHeading (FILE * fp);</span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="plaintext">void computeCorrelationMatrixPairwise(alignment_struct * alignment, clr_struct * omega, int omegaIndex, int firstRowIndex, void * threadData, cor_t ** myCorrelationMatrix, char * lookuptable);</span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="plaintext">void applyCorrelationMatrixAdditions (clr_struct * omega, int omegaIndex, int firstRowIndex, cor_t ** correlationMatrix);</span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="plaintext">void overlapCorrelationMatrixAdditions (alignment_struct * alignment, clr_struct * omega, int lvw_i, int cvw_i, int * firstRowToCopy, int * firstRowToCompute, int * firstRowToAdd);</span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="plaintext">void shiftCorrelationMatrixValues (clr_struct * omega, int lvw_i, int cvw_i, int firstRowToCopy, cor_t ** correlationMatrix);</span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="plaintext"></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="plaintext"></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="plaintext">void commandLineParser(int argc, char** argv, </span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="plaintext"> char * infile,</span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext"> char * sfsfile,</span>
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287
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="plaintext"> char * sfsofile,</span>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext"> char * sfofile, </span>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext"> int * grid, </span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="plaintext"> int * length, </span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="plaintext"> unsigned int * seed,</span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="plaintext"> int * fileFormat, </span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="plaintext"> int * results,</span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="plaintext"> char * outgroupName,</span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="plaintext"> unsigned char *userSetFolded,</span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="plaintext"> unsigned char * userSFS,</span>
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297
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="plaintext"> unsigned char * onlySFS,</span>
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298
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<pre style="margin: 0;">-<span id="LC298" class="line" lang="plaintext"> unsigned char * onlySF,</span>
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299
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="plaintext"> int * monomorphic,</span>
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300
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="plaintext"> int * threads,</span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="plaintext"> int * sequences,</span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="plaintext"> int * analyticalSFS,</span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="plaintext"> double *growthRate);</span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="plaintext"></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="plaintext">void removeMonomorphicSites (int monomorphic, FILE * fp);</span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="plaintext"></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="plaintext">t_sfs computeBaseLikelihood();</span>
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<td class="diff-line-num old old_line" data-linenumber="308" 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">
308
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="plaintext">t_sfs getAlpha (int sweepPosition, t_sfs * likelihood);</span>
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309
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="plaintext"></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="plaintext">int isBinary(char input);</span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="plaintext">void printIntArray(int *array, int n);</span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="plaintext">void printUCharArray(unsigned char *array, int n);</span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="plaintext">void printFloatArray(float *array, int n);</span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="plaintext">void printCharArray(char *array, int n);</span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="plaintext">int isEndOfLine(char ent);</span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="plaintext">void goToLineEnd(FILE *fp);</span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="plaintext">int findFirstAlignment(FILE *fp, int format);</span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="plaintext">int findNextAlignment(FILE *fp, int fileFormat);</span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="plaintext">void freeAlignment();</span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="plaintext">void readAlignment(FILE *fp, int format, FILE * fpInfo, FILE * sfO);</span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext">void compressAlignment(alignment_struct *alignment);</span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="plaintext">void knuthShuffle(int orgArray[], int arraySize, int start, int end);</span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="plaintext">int parseSample(FILE *fp, int targetTok, char **word, int *wordLength, int curTok);</span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="plaintext">void unGetChars(FILE *fp, char* chars, int n);</span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="plaintext">int isValidDNACharacter(char input);</span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="plaintext">void parseIndividual(char *word, char** genotype, char delimiter, int token, char* states, char phased, char unphased, int *ploidy, int *max_ploidy);</span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext">void ignoreAll(FILE * fp, char * ent);</span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="plaintext">int isSpace(char ent);</span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="plaintext">double XchooseY_ln(int x, int y);</span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="plaintext">void checkSNIPPositions (FILE* fp, alignment_struct * alignment, int index);</span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="plaintext">void createSFS (FILE * fpSFS, FILE * fpSFSo, int alignmentIndex, int * SFSsize);</span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="plaintext">void createCLR (int grid);</span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="plaintext">void createPROBS (int probGrid);</span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="plaintext">void createPatterns(void);</span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="plaintext">void computeFactLUT(void);</span>
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<pre style="margin: 0;">-<span id="LC358" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="plaintext">double gettime(void);</span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="plaintext">t_sfs likelihoodSFS_SNP(t_sfs * tmpSFS, int x, int n, unsigned char f, int c);</span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="plaintext">void updateSF(FILE * fpSFo);</span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC365" class="line" lang="plaintext">#ifdef _USE_PTHREADS</span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="plaintext">typedef struct</span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="plaintext">{</span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="plaintext"> int threadID;</span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="plaintext"> int threadTOTAL;</span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="plaintext"> int threadBARRIER;</span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="plaintext"> int threadOPERATION;</span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="plaintext">}threadData_t;</span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="plaintext">pthread_t * workerThreadL;</span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="plaintext">threadData_t * threadDataL;</span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="plaintext">int gridP;</span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="plaintext">void likelihoodSFS_thread(int tid, int threads);</span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="plaintext">void parallelComputationRVLUT_thread(int tid, int threads);</span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="plaintext">void computeAlpha_parallel(int grid);</span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="plaintext">void parallelComputationAlpha_thread(int tid, int threads);</span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="plaintext">void syncThreadsBARRIER();</span>
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386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="plaintext"></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="plaintext"></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="plaintext">#endif</span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="plaintext"></span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="plaintext">#ifdef _DO_CHECKPOINTS</span>
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<td class="diff-line-num old old_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="plaintext">double lastCheckpointTime;</span>
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<td class="diff-line-num old old_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="plaintext">double checkPointInterval;</span>
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<td class="diff-line-num old old_line" data-linenumber="393" 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">
393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="plaintext">extern void writeCheckpoint();</span>
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<td class="diff-line-num old old_line" data-linenumber="394" 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">
394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="plaintext">#endif</span>
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<td class="diff-line-num old old_line" data-linenumber="395" 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">
395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="plaintext">#endif</span></pre>
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