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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/discosnp">Debian Med / discosnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/commit/5d31fa2928d45f3c3b84b2afc3b28c7120176bcd">5d31fa29</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-01-27T14:14:14+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.4.3</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#cb5f0914b158384fc97934cc8fd6cba4e00b7d81">
discoSnpRAD/README.md
</a>
</li>
<li class="file-stats">
<a href="#2d703bba3f2486e5a5855a6fdc2f6c1e0d61ed3f">
discoSnpRAD/clustering_scripts/discoRAD_clustering.sh
</a>
</li>
<li class="file-stats">
<a href="#db843ee1aa7e62bf45356464a94f6f15cd7fbc69">
discoSnpRAD/run_discoSnpRad.sh
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/discosnp/commit/5d31fa2928d45f3c3b84b2afc3b28c7120176bcd#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" 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">@@ -10,7 +10,7 @@ cmake_minimum_required(VERSION 2.6)</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MAJOR 2<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MINOR 4<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_PATCH <span class="idiff left right">3</span><span class="p">)</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span> <span class="p">(</span>DEFINED MAJOR<span class="p">)</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span> <span class="p">(</span>gatb-tool_VERSION_MAJOR <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">MAJOR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,6 +84,7 @@ SET (CPACK_SOURCE_IGNORE_FILES</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cmake"><span class="p">)</span></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># For creating the BINARY package we include the files we want</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/discoSnpRAD DESTINATION .<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/doc DESTINATION .<span class="p">)</span></span>
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88
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/test DESTINATION .<span class="p">)</span></span>
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89
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INSTALL</span> <span class="p">(</span>DIRECTORY <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CURRENT_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/scripts DESTINATION . FILES_MATCHING REGEX <span class="s2" style="color: #d14;">".*</span><span class="se" style="color: #d14;">\\</span><span class="s2" style="color: #d14;">.(py|sh)$"</span> PATTERN <span class="s2" style="color: #d14;">"jenkins"</span> EXCLUDE<span class="p">)</span></span>
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<li id="cb5f0914b158384fc97934cc8fd6cba4e00b7d81">
<a href="https://salsa.debian.org/med-team/discosnp/commit/5d31fa2928d45f3c3b84b2afc3b28c7120176bcd#cb5f0914b158384fc97934cc8fd6cba4e00b7d81"><strong>discoSnpRAD/README.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,22 +11,25 @@ Gauthier, J., Mouden, C., Suchan, T., Alvarez, N., Arrigo, N., Riou, C., Lemait</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">*</span> discoSnp++</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">*</span> discoSnp++<span class="idiff left"> (see </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">../README.md</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">../README.md</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`short_read_connector`</span> must have been downloaded and installed (clustering task). <span class="p">[</span><span class="nv" style="color: #008080;">https://github.com/GATB/short_read_connector</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/GATB/short_read_connector</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown">./run_discoSnpRad.sh -<span class="idiff left right">-fof read_file_of_files --src_path <directory></span> [discoSnp++ OPTIONS]</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown">./run_discoSnpRad.sh -<span class="idiff left right">r read_file_of_files -S -p myDiscoSnpRADresult</span> [discoSnp++ OPTIONS]</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">Clustering</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Clustering option**</span> (RAD-specific option):</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown">-S|--src_path <directory></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"> **absolute** path to short_read_connector directory, containing the "short_read_connector.sh" file. </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">-S|--src [src_path]</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"> performs clustering of variants with short_read_connector</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"> src_path: **absolute** path to short_read_connector directory, containing the "short_read_connector.sh" file. </span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"> -Note1: short read connector must be compiled.</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"> -Note2: with this option, discoSnpRad provide a vcf file containing SNPs and INDELS, clustered by locus</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"> -Note2: if no value is given, it assumes short_read_connector.sh is in the PATH env variable.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"> -Note3: with this option, discoSnpRad outputs a vcf file containing the variants clustered by locus.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown">All other options are described in <span class="p">[</span><span class="nv" style="color: #008080;">discoSnp++ README</span><span class="p">](</span><span class="sx" style="color: #d14;">../README.md</span><span class="p">)</span>. Note that many discoSNP++ parameters have here default values, specifically adapted to RAD-seq data.</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">@@ -39,8 +42,33 @@ To see all options:</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Output</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="p">*</span> a log file reminds all filtering steps applied and the name of the output .vcf file</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"><span class="p">*</span> a vcf file containing results of filtering and clustering</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown">When run with output prefix name <span class="sb" style="color: #d14;">`myDiscoSnpRADresult`</span>, the main output file is :</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`myDiscoSnpRADresult_[parameter_values]_clustered.vcf`</span>: the final set of variants, with various information, including clustering per locus information (see VCF format below).</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">*</span> or <span class="sb" style="color: #d14;">`myDiscoSnpRADresult_[parameter_values].vcf`</span> if no clustering was performed.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">Additionnally, several other files are output that can be usefull :</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`myDiscoSnpRADresult_[parameter_values]_raw.fa`</span>: the raw set of variants in fasta format, prior to any filtering and clustering steps.</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`myDiscoSnpRADresult_[graph_parameter_values].h5`</span>: the de Bruijn graph in h5 format (reusable with any GATB tool)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`myDiscoSnpRADresult_read_files_correspondance.txt`</span>: the correspondence between read file names and IDs given as genotypes in the vcf</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">*</span> the standard output reminds all filtering steps applied and the name of the output .vcf file</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### VCF format</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">Each variant is described with: </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="p">*</span> an ID: <span class="sb" style="color: #d14;">`ID`</span> column, </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="p">*</span> two alleles (<span class="sb" style="color: #d14;">`REF`</span> and <span class="sb" style="color: #d14;">`ALT`</span> columns), </span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="p">*</span> a quality value: <span class="sb" style="color: #d14;">`INFO`</span> column, <span class="sb" style="color: #d14;">`Rk`</span>, between 0 (bad) and 1 (best),</span>
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66
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="p">*</span> some clustering information: <span class="sb" style="color: #d14;">`INFO`</span> field: with the locus id (<span class="sb" style="color: #d14;">`Cluster`</span>) and its number of varying sites (<span class="sb" style="color: #d14;">`ClSize`</span>),</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">*</span> and for each sample in the genotype columns (<span class="sb" style="color: #d14;">`G1`</span>, <span class="sb" style="color: #d14;">`G2`</span>,...): the inferred genotype (<span class="sb" style="color: #d14;">`0/0`</span>, <span class="sb" style="color: #d14;">`0/1`</span>, <span class="sb" style="color: #d14;">`1/1`</span>or <span class="sb" style="color: #d14;">`./.`</span>for missing value), the read depths (<span class="sb" style="color: #d14;">`RD`</span> total, <span class="sb" style="color: #d14;">`AD`</span>per allele), among others.</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"> </span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Content of this directory</span></span>
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<li id="2d703bba3f2486e5a5855a6fdc2f6c1e0d61ed3f">
<a href="https://salsa.debian.org/med-team/discosnp/commit/5d31fa2928d45f3c3b84b2afc3b28c7120176bcd#2d703bba3f2486e5a5855a6fdc2f6c1e0d61ed3f"><strong>discoSnpRAD/clustering_scripts/discoRAD_clustering.sh</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">@@ -22,7 +22,7 @@ echo "this script manages bubble clustering from a discofile.fa file, and the in</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" 1/ Remove variants with more than 95% missing genotypes and low rank (<0.4)"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" 2/ Cluster variants per locus"</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" 3/ Format the variants in a vcf file with cluster information"</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Usage: ./discoRAD_clustering.sh -f discofile -s SRC_<span class="idiff left right">directory/</span> -o output_file.vcf"</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Usage: ./discoRAD_clustering.sh -f discofile -s SRC_<span class="idiff left right">path</span> -o output_file.vcf"</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># echo "nb: all options are MANDATORY\n"</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"OPTIONS:"</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;"> -f: DiscoSnp fasta output containing coherent predictions"</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">@@ -44,7 +44,7 @@ while getopts "f:s:o:hw" opt; do</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"> s<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="shell"> <span class="nv" style="color: #008080;">short_read_connector_<span class="idiff left right">directory</span></span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="nv" style="color: #008080;">short_read_connector_<span class="idiff left right">path</span></span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$OPTARG</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell"> <span class="p">;;</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"> o<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">@@ -66,7 +66,7 @@ if [[ -z "${rawdiscofile}" ]]; then</td>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">red</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-f is mandatory</span><span class="nv" style="color: #008080;">$reset</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">short_read_connector_<span class="idiff left right">directory</span></span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="nt" style="color: #000080;">-z</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">short_read_connector_<span class="idiff left right">path</span></span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">red</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">-s is mandatory</span><span class="nv" style="color: #008080;">$reset</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">></span>&2</span>
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71
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit</span></span>
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72
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +80,7 @@ EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )</td>
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80
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-d</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$EDIR</span><span class="s2" style="color: #d14;">/../../build/"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="c" style="color: #998; font-style: italic;"># VERSION SOURCE COMPILED</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="shell"><span class="nv" style="color: #008080;">BINDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$EDIR</span><span class="s2" style="color: #d14;">"/../../build/bin"</span></span>
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span> <span class="c" style="color: #998; font-style: italic;"># VERSION BINARY</span></span>
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83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="shell"><span class="nv" style="color: #008080;">BINDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$EDIR</span><span class="s2" style="color: #d14;"><span class="idiff left right">"/../../bin"</span></span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="nv" style="color: #008080;">BINDIR</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$EDIR</span><span class="idiff left right">/../../bin</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="shell"><span class="nv" style="color: #008080;">rawdiscofile_base</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span> <span class="nb" style="color: #0086b3;">basename</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">rawdiscofile</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> .fa<span class="si" style="color: #d14;">)</span></span>
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86
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="shell"></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">@@ -150,7 +150,7 @@ fi</td>
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150
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#ls ${disco_simpler}.fa > ${disco_simpler}.fof</span></span>
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151
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="shell"></span>
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152
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Compute sequence similarities</span></span>
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153
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="shell"><span class="nv" style="color: #008080;">cmdSRC</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">short_read_connector_<span class="idiff left">directory</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/short_read_connector.sh</span> -b </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">disco_simpler</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.fa -q </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">disco_simpler</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.fof -s 0 -k </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">usedk</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> -a 1 -l -p </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">disco_simpler</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> 1>&2 "</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="shell"><span class="nv" style="color: #008080;">cmdSRC</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">short_read_connector_<span class="idiff left">path</span></span><span class="k" style="font-weight: 600;"><span class="idiff right">}</span></span><span class="s2" style="color: #d14;"> -b </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">disco_simpler</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.fa -q </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">disco_simpler</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.fof -s 0 -k </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">usedk</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> -a 1 -l -p </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">disco_simpler</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> 1>&2 "</span></span>
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$green$cmdSRC$cyan</span></span>
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155
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$wraith</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"false"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$cmdSRC</span></span>
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<li id="db843ee1aa7e62bf45356464a94f6f15cd7fbc69">
<a href="https://salsa.debian.org/med-team/discosnp/commit/5d31fa2928d45f3c3b84b2afc3b28c7120176bcd#db843ee1aa7e62bf45356464a94f6f15cd7fbc69"><strong>discoSnpRAD/run_discoSnpRad.sh</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">@@ -72,6 +72,7 @@ output_coverage_option=""</td>
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="shell"><span class="nv" style="color: #008080;">genotyping</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-genotype"</span></span>
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73
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="shell"><span class="nv" style="color: #008080;">remove</span><span class="o" style="font-weight: 600;">=</span>1</span>
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74
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="shell"><span class="nv" style="color: #008080;">verbose</span><span class="o" style="font-weight: 600;">=</span>1</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"><span class="nv" style="color: #008080;">clustering</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"false"</span></span>
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75
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="shell"><span class="nv" style="color: #008080;">short_read_connector_path</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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76
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="shell"><span class="nv" style="color: #008080;">option_phase_variants</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span></span>
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77
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#EDIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,17 +107,19 @@ function help {</td>
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106
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">" ************"</span></span>
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107
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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="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"run_discoSnpRad.sh, pipelining kissnp2 and kissreads and clustering per locus for calling SNPs and small indels from RAD-seq data without the need of a reference genome"</span></span>
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108
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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC109" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Version "</span><span class="nv" style="color: #008080;">$version</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Usage: ./run_discoSnpRad.sh --fof read_file_of_files --src<span class="idiff left right">_path <directory></span> [OPTIONS]"</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Usage: ./run_discoSnpRad.sh --fof read_file_of_files --src<span class="idiff left right"> [src_path]</span> [OPTIONS]"</span></span>
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110
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"MANDATORY"</span></span>
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111
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;"> -r|--fof <file name of a file of file(s)>"</span></span>
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112
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> The input read files indicated in a file of file(s)"</span></span>
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113
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> Example: -r bank.fof with bank.fof containing the two lines </span><span class="se" style="color: #d14;">\n\t\t\t</span><span class="s2" style="color: #d14;"> data_sample/reads_sequence1.fasta</span><span class="se" style="color: #d14;">\n\t\t\t</span><span class="s2" style="color: #d14;"> data_sample/reads_sequence2.fasta.gz"</span></span>
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114
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="shell"> </span>
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115
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">OPTIONS"</span></span>
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116
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<td class="diff-line-num new_line old" data-linenumber="117" 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="LC116" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;"> -S|--src_path <directory>"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="117" 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">
117
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<td class="diff-line-num new_line old" data-linenumber="117" 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="LC117" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> **absolute** path to short_read_connector directory, containing the </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">short_read_connector.sh</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> file. "</span></span>
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<td class="diff-line-num new old_line" data-linenumber="118" 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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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;"> -S|--src [src_path]"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> performs clustering of variants with short_read_connector"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="118" 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="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> src_path: **absolute** path to short_read_connector directory, containing the </span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;">short_read_connector.sh</span><span class="se" style="color: #d14;">\"</span><span class="s2" style="color: #d14;"> file. "</span></span>
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<td class="diff-line-num old_line" data-linenumber="118" 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">
118
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<td class="diff-line-num new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> -Note1: short read connector must be compiled."</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="119" 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">
119
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<td class="diff-line-num new_line old" data-linenumber="121" 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="LC119" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> -Note2: with this option, discoSnpRad provide a vcf file containing SNPs and INDELS, clustered by locus"</span> </span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> -Note2: if no value is given, it assumes short_read_connector.sh is in the PATH env variable."</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> -Note3: with this option, discoSnpRad outputs a vcf file containing the variants clustered by locus"</span> </span>
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120
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="shell"></span>
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121
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;"> -k | --k_size value <int value>"</span></span>
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122
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s2" style="color: #d14;"> Set the length of used kmers. Must fit the compiled value."</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" 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">@@ -184,15 +187,13 @@ while :; do</td>
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184
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="shell"> <span class="nt" style="color: #000080;">-w</span><span class="p">)</span></span>
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185
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="shell"> <span class="nv" style="color: #008080;">wraith</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"true"</span></span>
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186
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="shell"> <span class="p">;;</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="shell"> <span class="nt" style="color: #000080;">-S</span><span class="p">|</span><span class="nt" style="color: #000080;">--src_path</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="shell"> <span class="nt" style="color: #000080;">-S</span><span class="p">|</span><span class="nt" style="color: #000080;">--src</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="shell"> <span class="nv" style="color: #008080;">clustering</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"true"</span></span>
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188
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$2</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">2</span>:0:1<span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="c" style="color: #998; font-style: italic;"># checks that there exists a second value and its is not the start of the next option</span></span>
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189
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="shell"> <span class="nv" style="color: #008080;">short_read_connector_path</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$2</span></span>
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190
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">shift</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">else</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>die <span class="s1" style="color: #d14;">'ERROR: "'</span><span class="nv" style="color: #008080;">$1</span><span class="s1" style="color: #d14;">'" option requires a non-empty option argument.'</span></span>
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193
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="shell"><span class="nb" style="color: #0086b3;"> </span><span class="k" style="font-weight: 600;">fi</span></span>
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194
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="shell"> <span class="p">;;</span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="shell"></span>
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196
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="shell"> <span class="nt" style="color: #000080;">-a</span><span class="p">|</span><span class="nt" style="color: #000080;">--ambiguity_max_size</span><span class="p">)</span></span>
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197
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$2</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">[</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">2</span>:0:1<span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s2" style="color: #d14;">"-"</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="c" style="color: #998; font-style: italic;"># checks that there exists a second value and its is not the start of the next option</span></span>
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198
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="shell"> <span class="nv" style="color: #008080;">max_ambigous_indel</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: #008080;">$2</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -379,27 +380,40 @@ if [ -z "$read_sets" ]; then</td>
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379
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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380
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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381
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="shell"></span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="shell"><span class="nv" style="color: #008080;">src_file</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$short_read_connector_path</span><span class="s2" style="color: #d14;">/short_read_connector.sh"</span></span>
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383
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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$wraith</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"false"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$yellow</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">src_file</span><span class="k" style="font-weight: 600;">}</span><span class="nv" style="color: #008080;">$reset</span></span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#Checks if clustering can be performed</span></span>
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386
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="shell"></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$<span class="idiff left">wraith</span></span><span class="s2" style="color: #d14;"><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="s2" style="color: #d14;"><span class="idiff right">"fals</span>e"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$src_file</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">then</span></span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[[</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$wraith</span></span><span class="s2" style="color: #d14;"><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="s2" style="color: #d14;"><span class="idiff">"false"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num old old_line" data-linenumber="390" 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">
390
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<td class="diff-line-num new_line old" data-linenumber="385" 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="LC390" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> </span></span><span class="nb" style="color: #0086b3;"><span class="idiff">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">yellow</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="s2" style="color: #d14;"><span class="idiff">short_read_connector is </span></span><span class="nv" style="color: #008080;"><span class="idiff right">$src_file$reset</span></span><span class="s2" style="color: #d14;">"</span></span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="shell"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">fi</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left right">else</span></span></span>
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393
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<td class="diff-line-num new_line old" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left"> if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[[</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$wraith</span></span><span class="s2" style="color: #d14;"><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="s2" style="color: #d14;"><span class="idiff">"false"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">]]</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">then</span></span></span>
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394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left right"> </span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">red</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">**************************************************************************"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$<span class="idiff left">clustering</span></span><span class="s2" style="color: #d14;"><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="s2" style="color: #d14;"><span class="idiff right">"tru</span>e"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="shell"><span class="idiff left"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right"># first tests the directory given by user if any</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="387" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="shell"><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-n</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$short_read_connector_path</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="shell"><span class="k" style="font-weight: 600;"><span class="idiff left"> </span></span><span class="nv" style="color: #008080;"><span class="idiff">src_file</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$short_read_connector_path</span></span><span class="s2" style="color: #d14;"><span class="idiff right">/short_read_connector.sh</span>"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="shell"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">[</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$src_file</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">]</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">then</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left"> </span></span><span class="nb" style="color: #0086b3;"><span class="idiff">echo</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">yellow</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="s2" style="color: #d14;"><span class="idiff">short_read_connector path is </span></span><span class="nv" style="color: #008080;"><span class="idiff">$src_file$reset</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="shell"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">else</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="shell"><span class="k" style="font-weight: 600;"> <span class="idiff left right"> </span></span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">red</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">**************************************************************************"</span></span>
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395
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<td class="diff-line-num new_line" data-linenumber="393" 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">
393
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">** WARNING: I cannot find short_read_connector (-S). "</span></span>
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<td class="diff-line-num old_line" data-linenumber="396" 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">
396
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<td class="diff-line-num new_line" data-linenumber="394" 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">
394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">** </span><span class="nv" style="color: #008080;">$src_file</span><span class="s2" style="color: #d14;"> does not exist"</span></span>
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<td class="diff-line-num old_line" data-linenumber="397" 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">
397
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<td class="diff-line-num new_line" data-linenumber="395" 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">
395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">** I will not cluster variants per RAD locus"</span></span>
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<td class="diff-line-num old_line" data-linenumber="398" 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">
398
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<td class="diff-line-num new_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">**************************************************************************"</span></span>
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399
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$reset</span></span>
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400
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<td class="diff-line-num new_line old" data-linenumber="398" 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="LC400" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="shell"> <span class="nv" style="color: #008080;">clustering</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"false"</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="shell"><span class="k" style="font-weight: 600;"> else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="401" 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">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;">#then tests if src is in the PATH env variable</span></span>
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<td class="diff-line-num new new_line" data-linenumber="402" 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">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="shell"> <span class="nv" style="color: #008080;">src_file</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">command</span> <span class="nt" style="color: #000080;">-v</span> short_read_connector.sh<span class="si" style="color: #d14;">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="403" 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">
403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-n</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$src_file</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">yellow</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">short_read_connector path is </span><span class="nv" style="color: #008080;">$src_file$reset</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="405" 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">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="diff-line-num new new_line" data-linenumber="406" 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">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">red</span><span class="k" style="font-weight: 600;">}</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">**************************************************************************"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="407" 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">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">** WARNING: I cannot find short_read_connector in PATH. "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">** Try giving the absolute path of short_read_connector directory with option -S"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="401" 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="409" 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">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">** I will not cluster variants per RAD locus"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="410" 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">
410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t\t</span><span class="s2" style="color: #d14;">**************************************************************************"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="411" 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">
411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$reset</span></span>
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<td class="diff-line-num new new_line" data-linenumber="412" 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">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="shell"> <span class="nv" style="color: #008080;">clustering</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"false"</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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401
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="shell"><span class="k" style="font-weight: 600;"> fi</span></span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span> </span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="shell"> </span>
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403
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417
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="shell"></span>
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404
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="shell"></span>
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405
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">######### CHECK THE k PARITY ##########</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="643" 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="657" 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">@@ -643,13 +657,13 @@ echo -e "\t######## CLUSTERING PER LOCUS AND/OR FORMATTING ###############"</td>
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643
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657
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: #000080;">-e</span> <span class="s2" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s2" style="color: #d14;">###############################################################</span><span class="nv" style="color: #008080;">$reset</span><span class="s2" style="color: #d14;">"</span></span>
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644
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="shell"></span>
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645
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="shell"><span class="nv" style="color: #008080;">T</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">date</span> +%s<span class="si" style="color: #d14;">)</span><span class="s2" style="color: #d14;">"</span></span>
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646
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<pre style="margin: 0;">-<span id="LC646" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span><span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">-f</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$src_file</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff right"> </span><span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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660
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[<span class="idiff left">[</span></span><span class="idiff"> </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="nv" style="color: #008080;"><span class="idiff">$clustering</span></span><span class="s2" style="color: #d14;"><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="s2" style="color: #d14;"><span class="idiff">"true"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">]</span>]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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647
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661
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<pre style="margin: 0;"> <span id="LC661" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$wraith</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"false"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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648
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">yellow</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">Clustering and vcf formmatting</span><span class="nv" style="color: #008080;">$reset</span><span class="s2" style="color: #d14;">"</span></span>
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649
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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650
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">final_output</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">kissprefix</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_clustered.vcf"</span></span>
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651
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<pre style="margin: 0;">-<span id="LC651" class="line" lang="shell"> <span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$EDIR</span><span class="s2" style="color: #d14;">/clustering_scripts/discoRAD_clustering.sh -f </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">kissprefix</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_raw.fa -s </span><span class="nv" style="color: #008080;">$s<span class="idiff left right">hort_read_connector_path</span></span><span class="s2" style="color: #d14;"> -o </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">final_output</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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652
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$green$cmd$cyan</span></span>
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665
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="shell"> <span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$EDIR</span><span class="s2" style="color: #d14;">/clustering_scripts/discoRAD_clustering.sh -f </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">kissprefix</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_raw.fa -s </span><span class="nv" style="color: #008080;">$s<span class="idiff left right">rc_file</span></span><span class="s2" style="color: #d14;"> -o </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">final_output</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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666
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$green$cmd$cyan<span class="idiff left right">$reset</span></span></span>
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653
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667
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$wraith</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"false"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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654
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668
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$cmd</span></span>
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655
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669
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -668,7 +682,7 @@ else</td>
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668
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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669
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683
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">final_output</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">kissprefix</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.vcf"</span></span>
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670
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684
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="shell"> <span class="nv" style="color: #008080;">cmd</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"python3 </span><span class="nv" style="color: #008080;">$EDIR</span><span class="s2" style="color: #d14;">/../scripts/create_filtered_vcf.py -i </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">kissprefix</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">_raw.fa -o </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">final_output</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;"> -m 0.95 -r 0.4"</span></span>
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671
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$green$cmd$cyan</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$green$cmd$cyan<span class="idiff left right">$reset</span></span></span>
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672
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686
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="shell"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$wraith</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">"false"</span> <span class="o" style="font-weight: 600;">]]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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673
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687
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">eval</span> <span class="nv" style="color: #008080;">$cmd</span></span>
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674
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688
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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