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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/proteinortho">Debian Med / proteinortho</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2">6ecf7dce</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-21T08:33:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.16+dfsg</pre>
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<h4>12 changed files:</h4>
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#36a872632d316444cc5323d30503cc0b7ef33071">
manual.html
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<li class="file-stats">
<a href="#c3a57e7afe0f1aa9a980dfc188aa873d3c006ce0">
proteinortho5.pl
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<li class="file-stats">
<a href="#63ca7a8ee3bc533f40d25b4b217452dd3d054ed9">
proteinortho5_clean_edges2.pl
</a>
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<li class="file-stats">
<a href="#d7b44f60b1891297da292f87114cb80f89d8526f">
proteinortho5_clustering.cpp
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<li class="file-stats">
<a href="#b449ded4202264f363300e737ee12e8592179216">
test/C.faa
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<li class="file-stats">
<a href="#a11f8424ded8665fc5fda5e453ed096f53c16922">
test/E.faa
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<li class="file-stats">
<a href="#d721dd5b19dfc1f9af3ee33096db8d06c483873c">
test/L.faa
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<li class="file-stats">
<a href="#b4cb7401cf06d8f9e64d61ef65084716166606cb">
<span class="new-file">
+
tools/check_graph_duplicate_ids.pl
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<li class="file-stats">
<a href="#8311c5e5a1bdf4fa9564aa34ede64baef98d0ebb">
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+
tools/extract_from_graph.pl
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<li class="file-stats">
<a href="#ae7905f5a47b30d2a6e01ba97d24279fccbe00a8">
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+
tools/graph_conv.pl
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<li class="file-stats">
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+
tools/remove_graph_duplicates.pl
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<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,7 +2,7 @@</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="nv" style="color: teal;">INSTALLDIR</span><span class="o" style="font-weight: 600;">=</span>/usr/local/bin</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"><span class="nv" style="color: teal;">CPP</span> <span class="o" style="font-weight: 600;">=</span> g++</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-O<span class="idiff left right">3</span></span> <span class="nt" style="color: navy;">-Wno-unused-result</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="nv" style="color: teal;">CPPFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: navy;">-Wall</span> <span class="nt" style="color: navy;">-O<span class="idiff left">2</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">gnu++11</span> <span class="nt" style="color: navy;">-Wno-unused-result</span></span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">proteinortho5_clustering proteinortho5_tree</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#36a872632d316444cc5323d30503cc0b7ef33071"><strong>manual.html</strong></a>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="html"> <span class="nt" style="color: navy;"></head></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="html"><span class="nt" style="color: navy;"><body></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="html"><span class="nt" style="color: navy;"><h1></span>Proteinortho Manual / PoFF Manual<span class="nt" style="color: navy;"></h1></span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="html"><span class="nt" style="color: navy;"><small></span>This manual corresponds to version 5.1<span class="idiff left right">5</span><span class="nt" style="color: navy;"></small></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="html"><span class="nt" style="color: navy;"><small></span>This manual corresponds to version 5.1<span class="idiff left right">6</span><span class="nt" style="color: navy;"></small></span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Introduction<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="html">Proteinortho is a tool to detect orthologous genes within different species.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="html">For doing so, it compares similarities of given gene sequences and clusters them to find significant groups.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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="154" 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">@@ -154,17 +154,27 @@ They are:</td>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Hints<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="html"><span class="nt" style="color: navy;"><ul></span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>Using <span class="nt" style="color: navy;"><i></span>.faa<span class="nt" style="color: navy;"></i></span> to indicate that your file contains amino acids and <span class="nt" style="color: navy;"><i></span>.fna<span class="nt" style="color: navy;"></i></span> to show it contains nucleotides makes life much easier.</span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="html"><span class="nt" style="color: navy;"><li></span><span class="idiff left right">Each sequence ID in your FASTA files must be unique. Consider renaming the otherwise</span>.</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="html"><span class="nt" style="color: navy;"><li></span><span class="idiff left">Sequence IDs must be unique within a single FASTA file. Consider renaming otherwise. </span><span class="nt" style="color: navy;"><span class="idiff"><br></span></span><span class="idiff right">Note: Till version 5.15 sequences IDs had to be unique among the whole dataset. Proteinortho now keeps track of name and species to avoid the necessissity of renaming</span>.</span>
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158
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>You need write permissions in the directory of your FASTA files as Proteinortho will create blast databases. If this is not the case, consider using symbolic links to the FASTA files.</span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>The directory <span class="nt" style="color: navy;"><i></span>tools<span class="nt" style="color: navy;"></i></span> cotains useful tools, e.g. <span class="nt" style="color: navy;"><code></span>grab_proteins.pl<span class="nt" style="color: navy;"></code></span> which fetches protein sequences of orthologous groups from Proteinortho output table</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>The directory <span class="nt" style="color: navy;"><i></span>tools<span class="nt" style="color: navy;"></i></span> co<span class="idiff left right">n</span>tains useful tools, e.g. <span class="nt" style="color: navy;"><code></span>grab_proteins.pl<span class="nt" style="color: navy;"></code></span> which fetches protein sequences of orthologous groups from Proteinortho output table</span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="html"><span class="nt" style="color: navy;"></ul></span></span>
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="html"><span class="nt" style="color: navy;"><h2></span>Usage<span class="nt" style="color: navy;"></h2></span></span>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="html"><span class="nt" style="color: navy;"><code></span>proteinortho5.pl [OPTIONS] FASTA1 FASTA2 [FASTAn...]<span class="nt" style="color: navy;"></code></span> <span class="nt" style="color: navy;"><p></span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="html"></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="html"><span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">border=</span><span class="s" style="color: #d14;">"<span class="idiff left">1"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">cellspacing=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"0</span>"</span> <span class="na" style="color: teal;">cellpadding=</span><span class="s" style="color: #d14;">"2"</span><span class="nt" style="color: navy;">></span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="html"><span class="nt" style="color: navy;"><table</span> <span class="na" style="color: teal;">border=</span><span class="s" style="color: #d14;">"<span class="idiff left">0"</span></span><span class="idiff"> </span><span class="na" style="color: teal;"><span class="idiff">cellspacing=</span></span><span class="s" style="color: #d14;"><span class="idiff right">"2</span>"</span> <span class="na" style="color: teal;">cellpadding=</span><span class="s" style="color: #d14;">"2"</span><span class="nt" style="color: navy;">></span></span>
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166
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td><b></span>Option<span class="nt" style="color: navy;"></b></td><td><b></span>Default value<span class="nt" style="color: navy;"></b></td><td><b></span>Description<span class="nt" style="color: navy;"></b></td></tr></span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><hr><b></span>[General options]<span class="nt" style="color: navy;"></b><hr></td></tr></span></span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="html"></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-project=<span class="nt" style="color: navy;"></td><td></span>myproject<span class="nt" style="color: navy;"></td><td></span> prefix for all result file names<span class="nt" style="color: navy;"></td></tr></span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-cpus=<span class="nt" style="color: navy;"></td><td></span>auto<span class="nt" style="color: navy;"></td><td></span>use the given number of threads<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-verbose<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>give a lot of information about the current progress<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-keep<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>store temporary blast results for reuse (advisable for larger jobs)<span class="nt" style="color: navy;"></td></tr></span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-temp=<span class="nt" style="color: navy;"></td><td></span>working directory<span class="nt" style="color: navy;"></td><td></span> path for temporary files<span class="nt" style="color: navy;"></td></tr></span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-force<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>force recalculation of blast results in any case<span class="nt" style="color: navy;"></td></tr></span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-clean<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>remove all unnecessary files after processing<span class="nt" style="color: navy;"></td></tr></span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="html"></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><hr><b></span>[Search options]<span class="nt" style="color: navy;"></b><hr></td></tr></span></span>
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168
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-e=<span class="nt" style="color: navy;"></td><td></span>1e-05<span class="nt" style="color: navy;"></td><td></span>E-value for blast<span class="nt" style="color: navy;"></td></tr></span></span>
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169
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-p=<span class="nt" style="color: navy;"></td><td></span>blastp+<span class="nt" style="color: navy;"></td><td></span>blast program to use:</span>
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170
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="html"><span class="nt" style="color: navy;"><ul></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">@@ -179,29 +189,34 @@ in case you only have access to blast legacy:</td>
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179
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>blastp <span class="ni" style="color: purple;">→</span> sequences are given as amino acids</span>
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180
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>tblastx <span class="ni" style="color: purple;">→</span> sequences are given as nucleotides and will be interpreted as (translated) amino acids in all three reading frames</span>
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181
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="html"><span class="nt" style="color: navy;"></ul></span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="html"></span>
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185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-project=<span class="nt" style="color: navy;"></td><td></span>myproject<span class="nt" style="color: navy;"></td><td></span> prefix for all result file names<span class="nt" style="color: navy;"></td></tr></span></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-temp=<span class="nt" style="color: navy;"></td><td></span>working directory<span class="nt" style="color: navy;"></td><td></span> path for temporary files<span class="nt" style="color: navy;"></td></tr></span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-synteny<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>activate PoFF extension to separate similar sequences using synteny (requires a GFF file for each FASTA file)<span class="nt" style="color: navy;"></td></tr></span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-nograph<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>do not generate .graph files with pairwise orthology data<span class="nt" style="color: navy;"><br></span>saves some time<span class="nt" style="color: navy;"></td></tr></span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-keep<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>store temporary blast results for reuse<span class="nt" style="color: navy;"></td></tr></span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-clean<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>remove all unnecessary files after processing<span class="nt" style="color: navy;"></td></tr></span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-desc<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>write gene description file (XXX.descriptions); works only with NCBI-formated FASTA entries currently<span class="nt" style="color: navy;"></td></tr></span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-force<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>force recalculation of blast results in any case<span class="nt" style="color: navy;"></td></tr></span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-cpus=<span class="nt" style="color: navy;"></td><td></span>auto<span class="nt" style="color: navy;"></td><td></span>use the given number of threads<span class="nt" style="color: navy;"></td></tr></span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-selfblast<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>apply selfblast to directly paralogs; normally these are inferred indirectly from orthology data to other species (experimental!)<span class="nt" style="color: navy;"></td></tr></span></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-singles<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>Also report genes without orthologs in table output<span class="nt" style="color: navy;"></td></tr></span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-selfblast<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>apply selfblast to directly paralogs; normally these are inferred indirectly from orthology data to other species (experimental!)<span class="nt" style="color: navy;"></td></tr></span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-sim=<span class="nt" style="color: navy;"></td><td></span>0.95<span class="nt" style="color: navy;"></td><td></span>min. similarity for additional hits<span class="nt" style="color: navy;"></td></tr></span></span>
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196
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-identity=<span class="nt" style="color: navy;"></td><td></span>25<span class="nt" style="color: navy;"></td><td></span>min. percent identity of best blast alignments<span class="nt" style="color: navy;"></td></tr></span></span>
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197
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-cov=<span class="nt" style="color: navy;"></td><td></span>50<span class="nt" style="color: navy;"></td><td></span>min. coverage of best blast alignments in percent<span class="nt" style="color: navy;"></td></tr></span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-subpara=<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>additional parameters for blast; set these in quotes (e.g. -subpara='-seg no') <span class="nt" style="color: navy;"><br></span>This parameter was named -blastParameters in earlier versions<span class="nt" style="color: navy;"></td></tr></span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="html"></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="html"></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><hr><b></span>[Synteny options]<span class="nt" style="color: navy;"></b><hr></td></tr></span></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-synteny<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>activate PoFF extension to separate similar sequences using synteny (requires a GFF file for each FASTA file)<span class="nt" style="color: navy;"></td></tr></span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-dups=<span class="nt" style="color: navy;"></td><td></span>0<span class="nt" style="color: navy;"></td><td></span> applied in combination with -synteny; number of reiterations for adjacencies heuristic to determine duplicated regions; <span class="nt" style="color: navy;"><br></span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="html">if set to a higher number, co-orthologs will tend to get clustered together rather than getting separated</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-cs=<span class="nt" style="color: navy;"></td><td></span>3<span class="nt" style="color: navy;"></td><td></span> applied in combination with -synteny; size of a maximum common substring (MCS) for adjacency matches; <span class="nt" style="color: navy;"><br></span> the longer this value becomes the longer syntenic regions need to be in order to be detected <span class="nt" style="color: navy;"></td></tr></span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>alpha=<span class="nt" style="color: navy;"></td><td></span>0.5<span class="nt" style="color: navy;"></td><td></span>weight of adjacencies vs. sequence similarity<span class="nt" style="color: navy;"></td></tr></span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="html"></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><hr><b></span>[Clustering options]<span class="nt" style="color: navy;"></b><hr></td></tr></span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-singles<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>also report genes without orthologs in table output<span class="nt" style="color: navy;"></td></tr></span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-purity=<span class="nt" style="color: navy;"></td><td></span>1<span class="nt" style="color: navy;"></td><td></span>avoid spurious graph assignments [range: 0.01-1, default 0.75]<span class="nt" style="color: navy;"></td></tr></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-conn=<span class="nt" style="color: navy;"></td><td></span>0.1<span class="nt" style="color: navy;"></td><td></span>min. algebraic connectivity of orthologous groups during clustering<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-sim=<span class="nt" style="color: navy;"></td><td></span>0.95<span class="nt" style="color: navy;"></td><td></span>min. similarity for additional hits<span class="nt" style="color: navy;"></td></tr></span></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-blastpath=<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>path to your local blast installation (if not in present in default paths)<span class="nt" style="color: navy;"></td></tr></span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-blastParameters=<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>additional parameters for blast; set these in quotes (e.g. -blastParameters='-seg no')<span class="nt" style="color: navy;"></td></tr></span></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-verbose<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>give a lot of information about the current progress<span class="nt" style="color: navy;"></td></tr></span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-debug<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>gives detailed information for bug tracking<span class="nt" style="color: navy;"></td></tr></span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-nograph<span class="nt" style="color: navy;"></td><td></span>-<span class="nt" style="color: navy;"></td><td></span>do not generate .graph files with pairwise orthology data<span class="nt" style="color: navy;"><br></span>saves some time<span class="nt" style="color: navy;"></td></tr></span></span>
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204
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="html"></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><hr><b></span>[Misc options]<span class="nt" style="color: navy;"></b><hr></td></tr></span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-desc<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>write gene description file (XXX.descriptions); works only with NCBI-formated FASTA entries currently<span class="nt" style="color: navy;"></td></tr></span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-blastpath=<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>path to your local blast installation (if not in present in default paths)<span class="nt" style="color: navy;"></td></tr></span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-debug<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>gives detailed information for bug tracking<span class="nt" style="color: navy;"></td></tr></span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="html"></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><hr><b></span>[Large compute jobs]<span class="nt" style="color: navy;"></b><hr></td></tr></span></span>
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220
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><b></span>Parameters needed to distribute the runs over several machines<span class="nt" style="color: navy;"></b></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-step=<span class="nt" style="color: navy;"></td><td></span>0<span class="nt" style="color: navy;"></td><td></span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="html">perform only specific steps of the analysis</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">@@ -211,31 +226,32 @@ perform only specific steps of the analysis</td>
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211
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>3 <span class="ni" style="color: purple;">→</span> perform clustering</span>
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212
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>0 <span class="ni" style="color: purple;">→</span> perform all steps</span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="html"><span class="nt" style="color: navy;"></ul></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>startat=<span class="nt" style="color: navy;"></td><td></span>0<span class="nt" style="color: navy;"></td><td></span>file number to start with<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>stopat=<span class="nt" style="color: navy;"></td><td></span>-1<span class="nt" style="color: navy;"></td><td></span>file number to end with (very last one = -1)<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td</span> <span class="na" style="color: teal;">colspan=</span><span class="s" style="color: #d14;">3</span><span class="nt" style="color: navy;">><b></span>Parameters applied in combination with -synteny<span class="nt" style="color: navy;"><b></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-dups=<span class="nt" style="color: navy;"></td><td></span>0<span class="nt" style="color: navy;"></td><td></span> applied in combination with -synteny; number of reiterations for adjacencies heuristic to determine duplicated regions; <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="html">if set to a higher number, co-orthologs will tend to get clustered together rather than getting separated</span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="html"><span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>-cs=<span class="nt" style="color: navy;"></td><td></span>3<span class="nt" style="color: navy;"></td><td></span> applied in combination with -synteny; size of a maximum common substring (MCS) for adjacency matches; <span class="nt" style="color: navy;"><br></span> the longer this value becomes the longer syntenic regions need to be in order to be detected <span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>alpha=<span class="nt" style="color: navy;"></td><td></span>0.5<span class="nt" style="color: navy;"></td><td></span>weight of adjacencies vs. sequence similarity<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="html"><span class="nt" style="color: navy;"><tr><td></span>jobs=N/M<span class="nt" style="color: navy;"></td><td></span> <span class="nt" style="color: navy;"></td><td></span>distribute blast step into M subsets and run job number N out of M in this very process, only works in combination with -step=2<span class="nt" style="color: navy;"></td></tr></span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="html"><span class="nt" style="color: navy;"></table></span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="html"><span class="nt" style="color: navy;"><h3></span>Using several machines<span class="nt" style="color: navy;"></h3></span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="html">If you want to involve multiple machines or separate a Proteinortho run into smaller chunks, use the <span class="nt" style="color: navy;"><i></span>-<span class="idiff left right">steps=</span><span class="nt" style="color: navy;"></i></span> option.</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="html">If you want to involve multiple machines or separate a Proteinortho run into smaller chunks, use the <span class="nt" style="color: navy;"><i></span>-<span class="idiff left right">jobs=M/N</span><span class="nt" style="color: navy;"></i></span> option.</span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="html">First, run <span class="nt" style="color: navy;"><code></span>proteinortho5.pl -steps=1 ...<span class="nt" style="color: navy;"></code></span> to generate the indices.</span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="html">Then you can run <span class="nt" style="color: navy;"><code></span>proteinortho5.pl -steps=2 -startat=X -stopat=Y ...<span class="nt" style="color: navy;"></code></span> to run small chunks separately.</span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="html">Instead of X and Y numbers must be set representing the file number to be calculated. X and Y can be equal.</span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="html">E.g. you have four fasta files, the you can to run <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="html">Then you can run <span class="nt" style="color: navy;"><code></span>proteinortho5.pl -steps=2 -jobs=M/N ...<span class="nt" style="color: navy;"></code></span> to run small chunks separately.</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="html">Instead of M and N numbers must be set representing the number of jobs you want to divide the run into (M) and the job division to be performed by the process.</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="html">E.g. to divide a Proteinortho run into 4 jobs to run on several machines, use <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="html"></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="html"><span class="nt" style="color: navy;"><code></span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="html">proteinortho5.pl -steps=1 ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="html">on a single PC, then <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="html"><span class="nt" style="color: navy;"><code></span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">startat=0 -stopat=0</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">startat=1 -stopat=1</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">startat=2 -stopat=2</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">startat=3 -stopat=3</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">jobs=1/4</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">jobs=2/4</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">jobs=3/4</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="html">proteinortho5.pl -steps=2 -<span class="idiff left right">jobs=4/4</span> ... <span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="html"><span class="nt" style="color: navy;"></code></span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="html">seperateltly on different machines (within the same shared working directory).</span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="html">After all step 2 runs are done, <span class="nt" style="color: navy;"><code></span>proteinortho5.pl -steps=3 ...<span class="nt" style="color: navy;"></code></span> can be executed to perform the clustering and merge all calculations.</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="html">separately on different machines (can be run in parallel or iteratively within the same shared working directory).</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="html">After all step 2 runs are done, run </span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="html"><span class="nt" style="color: navy;"><br><code></span>proteinortho5.pl -steps=3 ...<span class="nt" style="color: navy;"></code></span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="html"><span class="nt" style="color: navy;"><br></span> to perform the clustering and merge all calculations on a single PC.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,7 +30,7 @@</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @authors Marcus Lechner, Clemens Elias Thoelken</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @email lechner@staff.uni-marburg.de</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @company University of Maruburg</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date 201<span class="idiff left right">6-08-26</span></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># @date 201<span class="idiff left right">7-04-18</span></span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"></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">@@ -47,7 +47,7 @@ use Thread::Queue;</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Variables</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5.1<span class="idiff left right">5</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"5.1<span class="idiff left right">6</span>"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$step</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1/2/3 -> do all / only apply step 1 / only apply step 2 / only apply step 3</span></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1 -> don't / be verbose</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0/1 -> don't / show debug data</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">@@ -60,14 +60,15 @@ our $alpha = 0.5; # Alpha value for ffadj_mcs.py</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$connectivity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;"># Algebr. connectivity threshold</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># 0 = autodetect</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$evalue</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1e-05"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$purity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.75</span><span class="p">;</span></span>
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63
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">50</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Percent coverage threshold for two proteins</span></span>
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64
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$identity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">25</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Percent identity threshold for two proteins</span></span>
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65
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$blastmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"blastp+"</span><span class="p">;</span></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="perl"><span class="c1" style="color: #998; font-style: italic;">#our $tmpdir = "./"; # Dir for tmp-files</span></span>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.95</span><span class="p">;</span></span>
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68
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$report</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$startat</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="p"><span class="idiff right">;</span></span></span>
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70
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><span class="idiff left">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">;</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$startat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">undef</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># removed 5.16</span></span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">undef</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># removed 5.16</span></span></span>
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71
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$keep</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$force</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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73
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -98,6 +99,12 @@ our $run_id = "";</td>
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98
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">%gene_counter</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Holds the number of genes for each data file (for sorting)</span></span>
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99
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$threads_per_process</span> <span class="p">:</span><span class="nv" style="color: teal;">shared</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Number of subthreads for blast</span></span>
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100
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Split work</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$part</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="perl"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"></span>
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101
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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102
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Parameters</span></span>
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103
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" 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="124" 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">@@ -117,6 +124,7 @@ foreach my $option (@ARGV) {</td>
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117
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cpus=(\d*)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
118
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cpus=auto$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span></span>
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119
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?alpha=([0-9\.]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$alpha</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?purity=([0-9\.]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$purity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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120
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?report=([0-9]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$report</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span> </span>
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121
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?conn=([0-9\.]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$connectivity</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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122
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?cov=([0-9]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$coverage</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" 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="134" 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">@@ -126,6 +134,7 @@ foreach my $option (@ARGV) {</td>
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126
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?sim=([0-9\.]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$sim</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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127
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?startat=([0-9]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$startat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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128
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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?stopat=([0-9]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?jobs?=([\d]+)\/([\d]+)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="nv" style="color: teal;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$2</span><span class="p">;</span> <span class="p">}</span> </span>
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129
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?selfblast$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span> </span>
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130
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?selfblast=(0|1)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$selfblast</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span> </span>
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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
131
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140
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?singles$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$singles</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="145" 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="154" 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">@@ -145,7 +154,7 @@ foreach my $option (@ARGV) {</td>
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145
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?graph/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$nograph</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="p">}</span> </span>
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<td class="diff-line-num old_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
146
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155
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?desc/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$desc</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span> </span>
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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
147
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?project=(.*)$/</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$project</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?<span class="idiff left right">blastParameters</span>=(.*)$/i</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$blastOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">m/^--?<span class="idiff left right">subpara</span>=(.*)$/i</span><span class="p">)</span> <span class="p">{</span> <span class="nv" style="color: teal;">$blastOptions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;}</span></span>
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<td class="diff-line-num old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
149
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="perl"> <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: teal;">$option</span> <span class="o" style="font-weight: 600;">!~</span> <span class="sr" style="color: #009926;">/^-/</span><span class="p">)</span> <span class="p">{</span> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">,</span><span class="nv" style="color: teal;">$option</span><span class="p">);</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
150
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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">print_usage</span><span class="p">();</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Invalid command line option: \'$option\'!\n"</span><span class="p">;</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="151" 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">
151
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" 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="162" 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">@@ -153,13 +162,23 @@ foreach my $option (@ARGV) {</td>
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153
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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154
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Check parameters</span></span>
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155
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<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">##########################################################################################</span></span>
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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$startat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$step</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Parameters -startat and -stopat only work for step 2!"</span><span class="p">);</span></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="perl"> <span class="p">}</span></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="perl"> <span class="nv" style="color: teal;">$run_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"_$startat-$stopat"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$startat</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$stopat</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Sorry, -startat and -stopat were removed. Please use -jobs=M/N for more flexible job splitting."</span><span class="p">);</span> </span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="perl"><span class="p">}</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="161" 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="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Job parameter use incorrectly. Number of jobs cannot be 0. Valid format: M/N"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="161" 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="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$split_to_X_jobs</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Job parameter use incorrectly. Job number cannot be 0 or greater than number of jobs. Valid format: M/N"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$step</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Parameter -jobs only works for step 2!"</span><span class="p">);}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="perl"> <span class="nv" style="color: teal;">$run_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"_$jobnumber"</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$split_to_X_jobs</span><span class="p">;</span></span>
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161
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<td class="diff-line-num new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="162" 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">
162
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="163" 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="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="perl"></span>
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163
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<td class="diff-line-num new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$simgraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$project.blast-graph$run_id"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Output file graph</span></span>
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<td class="diff-line-num old_line" data-linenumber="164" 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">
164
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<td class="diff-line-num new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="perl"><span class="k" style="font-weight: 600;">our</span> <span class="nv" style="color: teal;">$syngraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"$project.ffadj-graph$run_id"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Output file synteny</span></span>
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165
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="175" 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="194" 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">@@ -175,7 +194,7 @@ our $desctable = "$project.descriptions"; # Output file seq descriptions</td>
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175
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="perl"></span>
</pre>
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176
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">e</span> <span class="s" style="color: #d14;">"$project.proteinortho"</span><span class="p">)</span> <span class="p">{</span></span>
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177
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"!!!\nWarning: Data files for project '$project' already exists. Previous output files might be overwritten.\n"</span><span class="p">;</span></span>
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178
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<pre style="margin: 0;">-<span id="LC178" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Press CTRL + C to prevent me from proceeding<span class="idiff left right">)</span>\nWaiting for 10 seconds...\n!!!\n"</span><span class="p">;</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Press CTRL + C to prevent me from proceeding\nWaiting for 10 seconds...\n!!!\n"</span><span class="p">;</span></span>
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179
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">10</span><span class="p">);</span></span>
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180
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\nWell then, proceeding...\n\n"</span><span class="p">;</span></span>
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181
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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="209" 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">@@ -190,7 +209,7 @@ if (-e "$project.proteinortho") {</td>
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190
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Always do</span></span>
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191
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="perl"><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">check_files</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># Check files, count sequences</span></span>
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192
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="perl"><span class="nv" style="color: teal;">@files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">();</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">{</span> <span class="nv" style="color: teal;"><span class="idiff left">$gene_counter</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$b</span></span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="sr" style="color: #009926;"><span class="idiff"><=></span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$gene_counter</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$a</span></span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">keys</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">%gene_counter</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">push</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">@files</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">);}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># Biggest first</span></span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">{</span> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$gene_counter</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$a</span></span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$gene_counter</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$b</span></span><span class="p"><span class="idiff">})</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$a</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">cmp</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$b</span></span><span class="p"><span class="idiff">;}</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$gene_counter</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$b</span></span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="sr" style="color: #009926;"><span class="idiff"><=></span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$gene_counter</span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$a</span></span><span class="p"><span class="idiff">};}</span></span><span class="idiff"> </span><span class="p"><span class="idiff">}</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">keys</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">%gene_counter</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">push</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">@files</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$file</span></span><span class="p"><span class="idiff">);}</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># Biggest first # Alphabet otherwise 5.16</span></span></span>
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194
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213
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="perl"></span>
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195
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="perl"></span>
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196
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Step 1, check files and make indices</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="246" 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="265" 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">@@ -246,36 +265,36 @@ sub clean {</td>
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246
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="perl"></span>
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247
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">cluster</span> <span class="p">{</span></span>
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248
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<td class="diff-line-num new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Clustering by similarity (Proteinortho mode)\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="249" 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">
249
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<td class="diff-line-num new_line old" data-linenumber="268" 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="LC249" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_clustering -verbose $verbose -conn $connectivity -rmgraph '$rm_simgraph' $simgraph* >'$simtable'"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="250" 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="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_clustering -verbose $verbose -conn $connectivity -<span class="idiff left right">purity $purity -</span>rmgraph '$rm_simgraph' $simgraph* >'$simtable'"</span><span class="p">);</span></span>
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250
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<td class="diff-line-num new_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$singles</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
251
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<td class="diff-line-num new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Adding singles...\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
252
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<td class="diff-line-num new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fastas</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"' '"</span><span class="p">,</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"'"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="253" 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">
253
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<td class="diff-line-num new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_singletons.pl $fastas <'$simtable' >>'$simtable'"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="254" 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">
254
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<td class="diff-line-num new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="255" 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">
255
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<td class="diff-line-num new_line old" data-linenumber="274" 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="LC255" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">-> Output</span> written to $simtable\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="256" 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="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">[OUTPUT] -></span> written to $simtable\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
256
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<td class="diff-line-num new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$nograph</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="257" 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">
257
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<td class="diff-line-num new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Writing graph...\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="258" 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">
258
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<td class="diff-line-num new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># system("$po_path/proteinortho5_clean_edges -e '$rm_simgraph' $simgraph* >'$csimgraph'");</span></span>
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<td class="diff-line-num old_line" data-linenumber="259" 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">
259
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<td class="diff-line-num new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_clean_edges2.pl '$rm_simgraph' $simgraph* >'$csimgraph'"</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="260" 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">
260
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<td class="diff-line-num new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$keep</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: teal;">$rm_simgraph</span><span class="p">);}</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="261" 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">
261
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<td class="diff-line-num new_line old" data-linenumber="280" 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="LC261" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">-> Output</span> written to $csimgraph\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="262" 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="280" 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">
280
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC280" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">[OUTPUT] -></span> written to $csimgraph\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="262" 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">
262
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<td class="diff-line-num new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="263" 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">
263
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<td class="diff-line-num new_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="264" 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">
264
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<td class="diff-line-num new_line" data-linenumber="283" 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">
283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$synteny</span><span class="p">)</span> <span class="p">{</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="265" 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">
265
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<td class="diff-line-num new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\nClustering by gene-order (POFF mode)\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="266" 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">
266
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<td class="diff-line-num new_line old" data-linenumber="285" 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="LC266" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_clustering -verbose $verbose -conn $connectivity -rmgraph '$rm_syngraph' $syngraph* >'$syntable'"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="267" 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="285" 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">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_clustering -verbose $verbose -conn $connectivity -<span class="idiff left right">purity $purity -</span>rmgraph '$rm_syngraph' $syngraph* >'$syntable'"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
267
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<td class="diff-line-num new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$singles</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
268
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<td class="diff-line-num new_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Adding singles...\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
269
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<td class="diff-line-num new_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fastas</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"'"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"' '"</span><span class="p">,</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"'"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="270" 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">
270
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<td class="diff-line-num new_line" data-linenumber="289" 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">
289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_singletons.pl $fastas <'$syntable' >>'$syntable'"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="271" 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">
271
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<td class="diff-line-num new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="272" 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">
272
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<td class="diff-line-num new_line old" data-linenumber="291" 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="LC272" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">-> Output</span> written to $syntable\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="273" 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="291" 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">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">[OUTPUT] -></span> written to $syntable\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
273
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<td class="diff-line-num new_line" data-linenumber="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$nograph</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="274" 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">
274
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<td class="diff-line-num new_line" data-linenumber="293" 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">
293
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Writing graph...\n"</span><span class="p">;</span></span>
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275
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<td class="diff-line-num new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># system("$po_path/proteinortho5_clean_edges -e '$rm_syngraph' $syngraph* >'$csyngraph'");</span></span>
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276
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<td class="diff-line-num new_line" data-linenumber="295" 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">
295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$po_path/proteinortho5_clean_edges2.pl '$rm_syngraph' $syngraph* >'$csyngraph'"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="277" 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">
277
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<td class="diff-line-num new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$keep</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: teal;">$rm_syngraph</span><span class="p">);}</span></span>
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278
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<td class="diff-line-num new_line old" data-linenumber="297" 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="LC278" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">-> Output</span> written to $csyngraph\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="279" 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="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">[OUTPUT] -></span> written to $csyngraph\n"</span><span class="p">;</span></span>
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279
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<td class="diff-line-num new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="perl"> <span class="p">}</span></span>
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280
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<td class="diff-line-num new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="perl"> <span class="p">}</span></span>
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281
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="290" 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="309" 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">@@ -290,11 +309,32 @@ sub print_usage {</td>
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290
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<td class="diff-line-num new_line" data-linenumber="309" 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">
309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"JUS"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="291" 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">
291
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310
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="perl"></span>
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292
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<td class="diff-line-num new_line" data-linenumber="311" 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">
311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="perl"><span class="nv" style="color: teal;">Usage:</span> <span class="nv" style="color: teal;">proteinortho5</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">pl</span> <span class="p">[</span><span class="nv" style="color: teal;">OPTIONS</span><span class="p">]</span> <span class="nv" style="color: teal;">FASTA1</span> <span class="nv" style="color: teal;">FASTA2</span> <span class="p">[</span><span class="nv" style="color: teal;">FASTA</span><span class="o" style="font-weight: 600;">...</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="293" 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">
293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="perl"><span class="nv" style="color: teal;">Options:</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">e</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">E</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">value</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">blast</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="mf" style="color: #099;">1e-05</span><span class="p">]</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">p</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">program</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="nv" style="color: teal;">blastp</span><span class="o" style="font-weight: 600;">+</span><span class="p">]</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="perl"> <span class="p">{</span><span class="nv" style="color: teal;">blastn</span><span class="o" style="font-weight: 600;">|</span><span class="nv" style="color: teal;">blastp</span><span class="o" style="font-weight: 600;">|</span><span class="nv" style="color: teal;">tblastx</span><span class="o" style="font-weight: 600;">|</span><span class="nv" style="color: teal;">blastn</span><span class="o" style="font-weight: 600;">+|</span><span class="nv" style="color: teal;">blastp</span><span class="o" style="font-weight: 600;">+|</span><span class="nv" style="color: teal;">tblastx</span><span class="o" style="font-weight: 600;">+</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="perl"><span class="nv" style="color: teal;">Options:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="313" 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">
313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: teal;">General</span> <span class="nv" style="color: teal;">options</span><span class="p">]</span></span>
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296
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<td class="diff-line-num new_line" data-linenumber="314" 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">
314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">project</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">prefix</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">all</span> <span class="nv" style="color: teal;">result</span> <span class="nv" style="color: teal;">file</span> <span class="nv" style="color: teal;">names</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="nv" style="color: teal;">myproject</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">cpus</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">number</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">processors</span> <span class="nv" style="color: teal;">to</span> <span class="k" style="font-weight: 600;">use</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="nv" style="color: teal;">auto</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">verbose</span> <span class="nv" style="color: teal;">keeps</span> <span class="nv" style="color: teal;">you</span> <span class="nv" style="color: teal;">informed</span> <span class="nv" style="color: teal;">about</span> <span class="nv" style="color: teal;">the</span> <span class="nv" style="color: teal;">progress</span></span>
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297
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">temp</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">path</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">temporary</span> <span class="nv" style="color: teal;">files</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="nv" style="color: teal;">working</span> <span class="nv" style="color: teal;">directory</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">keep</span> <span class="nv" style="color: teal;">stores</span> <span class="nv" style="color: teal;">temporary</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">results</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">reuse</span></span>
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<td class="diff-line-num new new_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">force</span> <span class="nv" style="color: teal;">forces</span> <span class="nv" style="color: teal;">recalculation</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">results</span> <span class="nv" style="color: teal;">in</span> <span class="nv" style="color: teal;">any</span> <span class="k" style="font-weight: 600;">case</span></span>
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<td class="diff-line-num new new_line" data-linenumber="320" 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">
320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">clean</span> <span class="nv" style="color: teal;">remove</span> <span class="nv" style="color: teal;">all</span> <span class="nv" style="color: teal;">unnecessary</span> <span class="nv" style="color: teal;">files</span> <span class="nv" style="color: teal;">after</span> <span class="nv" style="color: teal;">processing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="321" 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">
321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">step</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">generate</span> <span class="nv" style="color: teal;">indices</span></span>
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<td class="diff-line-num new new_line" data-linenumber="322" 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">
322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="perl"> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">run</span> <span class="nv" style="color: teal;">blast</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">ff</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">adj</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">synteny</span> <span class="nv" style="color: teal;">is</span> <span class="nv" style="color: teal;">set</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="323" 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">
323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="perl"> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">clustering</span></span>
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<td class="diff-line-num new new_line" data-linenumber="324" 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">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">all</span> <span class="p">(</span><span class="nv" style="color: teal;">default</span><span class="p">)</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: teal;">Search</span> <span class="nv" style="color: teal;">options</span><span class="p">]</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">p</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">program</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="nv" style="color: teal;">blastp</span><span class="o" style="font-weight: 600;">+</span><span class="p">]</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">e</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">E</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">value</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">blast</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="mf" style="color: #099;">1e-05</span><span class="p">]</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="perl"> <span class="p">{</span><span class="nv" style="color: teal;">blastn</span><span class="o" style="font-weight: 600;">|</span><span class="nv" style="color: teal;">blastp</span><span class="o" style="font-weight: 600;">|</span><span class="nv" style="color: teal;">tblastx</span><span class="o" style="font-weight: 600;">|</span><span class="nv" style="color: teal;">blastn</span><span class="o" style="font-weight: 600;">+|</span><span class="nv" style="color: teal;">blastp</span><span class="o" style="font-weight: 600;">+|</span><span class="nv" style="color: teal;">tblastx</span><span class="o" style="font-weight: 600;">+</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="330" 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">
330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">selfblast</span> <span class="nv" style="color: teal;">apply</span> <span class="nv" style="color: teal;">selfblast</span><span class="p">,</span> <span class="nv" style="color: teal;">detects</span> <span class="nv" style="color: teal;">paralogs</span> <span class="nv" style="color: teal;">without</span> <span class="nv" style="color: teal;">orthologs</span></span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">sim</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">min</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">similarity</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">additional</span> <span class="nv" style="color: teal;">hits</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">..</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="mf" style="color: #099;">0.95</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="332" 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">
332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">identity</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">min</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">percent</span> <span class="nv" style="color: teal;">identity</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">best</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">hits</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="mi" style="color: #099;">25</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="333" 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">
333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">cov</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">min</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">coverage</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">best</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">alignments</span> <span class="nv" style="color: teal;">in</span> <span class="nv" style="color: teal;">%</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="nv" style="color: teal;">default:</span> <span class="mi" style="color: #099;">50</span><span class="p">]</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">subpara</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">additional</span> <span class="nv" style="color: teal;">parameters</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">the</span> <span class="nv" style="color: teal;">search</span> <span class="nv" style="color: teal;">tool</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="perl"> <span class="nv" style="color: teal;">example</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">subpara</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'-seg no'</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="perl"></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: teal;">Synteny</span> <span class="nv" style="color: teal;">options</span><span class="p">]</span></span>
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298
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">synteny</span> <span class="nv" style="color: teal;">activate</span> <span class="nv" style="color: teal;">PoFF</span> <span class="nv" style="color: teal;">extension</span> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">separate</span> <span class="nv" style="color: teal;">similar</span> <span class="nv" style="color: teal;">sequences</span></span>
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299
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="perl"> <span class="nv" style="color: teal;">by</span> <span class="nv" style="color: teal;">contextual</span> <span class="nv" style="color: teal;">adjacencies</span> <span class="p">(</span><span class="nv" style="color: teal;">requires</span> <span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">gff</span> <span class="k" style="font-weight: 600;">for</span> <span class="nb" style="color: #0086b3;">each</span> <span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">fasta</span><span class="p">)</span></span>
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300
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">dups</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">PoFF:</span> <span class="nv" style="color: teal;">number</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">reiterations</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">adjacencies</span> <span class="nv" style="color: teal;">heuristic</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="303" 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="343" 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">@@ -303,33 +343,30 @@ Options: -e= E-value for blast [default: 1e-05]</td>
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303
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="perl"> <span class="nv" style="color: teal;">adjacency</span> <span class="nv" style="color: teal;">matches</span> <span class="p">(</span><span class="nv" style="color: teal;">default:</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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304
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">alpha</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">PoFF:</span> <span class="nv" style="color: teal;">weight</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">adjacencies</span> <span class="nv" style="color: teal;">vs</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">sequence</span> <span class="nv" style="color: teal;">similarity</span></span>
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<td class="diff-line-num old_line" data-linenumber="305" 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">
305
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">default:</span> <span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">desc</span> <span class="nb" style="color: #0086b3;">write</span> <span class="nv" style="color: teal;">description</span> <span class="nv" style="color: teal;">files</span> <span class="p">(</span><span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">NCBI</span> <span class="nv" style="color: teal;">FASTA</span> <span class="nv" style="color: teal;">input</span> <span class="nv" style="color: teal;">only</span><span class="p">)</span></span>
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307
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">keep</span> <span class="nv" style="color: teal;">stores</span> <span class="nv" style="color: teal;">temporary</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">results</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">reuse</span></span>
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<td class="diff-line-num old old_line" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
308
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<td class="diff-line-num new_line old" data-linenumber="346" 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="LC308" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">force</span> <span class="nv" style="color: teal;">forces</span> <span class="nv" style="color: teal;">recalculation</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">results</span> <span class="nv" style="color: teal;">in</span> <span class="nv" style="color: teal;">any</span> <span class="k" style="font-weight: 600;">case</span></span>
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309
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<td class="diff-line-num new_line old" data-linenumber="346" 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="LC309" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">cpus</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">number</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">processors</span> <span class="nv" style="color: teal;">to</span> <span class="k" style="font-weight: 600;">use</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="nv" style="color: teal;">auto</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">selfblast</span> <span class="nv" style="color: teal;">apply</span> <span class="nv" style="color: teal;">selfblast</span><span class="p">,</span> <span class="nv" style="color: teal;">detects</span> <span class="nv" style="color: teal;">paralogs</span> <span class="nv" style="color: teal;">without</span> <span class="nv" style="color: teal;">orthologs</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="347" 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">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: teal;">Clustering</span> <span class="nv" style="color: teal;">options</span><span class="p">]</span></span>
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311
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<td class="diff-line-num new_line" data-linenumber="348" 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">
348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">singles</span> <span class="nv" style="color: teal;">report</span> <span class="nv" style="color: teal;">singleton</span> <span class="nv" style="color: teal;">genes</span> <span class="nv" style="color: teal;">without</span> <span class="nv" style="color: teal;">any</span> <span class="nv" style="color: teal;">hit</span></span>
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<td class="diff-line-num old old_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">identity</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">min</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">percent</span> <span class="nv" style="color: teal;">identity</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">best</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">hits</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="mi" style="color: #099;">25</span><span class="p">]</span></span>
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313
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">cov</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">min</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">coverage</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">best</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">alignments</span> <span class="nv" style="color: teal;">in</span> <span class="nv" style="color: teal;">%</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span><span class="nv" style="color: teal;">default:</span> <span class="mi" style="color: #099;">50</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="349" 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">
349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">purity</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">avoid</span> <span class="nv" style="color: teal;">spurious</span> <span class="nv" style="color: teal;">graph</span> <span class="nv" style="color: teal;">assignments</span> <span class="p">[</span><span class="mf" style="color: #099;">0.01</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nv" style="color: teal;">default</span> <span class="mf" style="color: #099;">0.75</span><span class="p">]</span></span>
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314
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<td class="diff-line-num new_line" data-linenumber="350" 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">
350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">conn</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">min</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">algebraic</span> <span class="nv" style="color: teal;">connectivity</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="mf" style="color: #099;">0.1</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="315" 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">
315
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<td class="diff-line-num new_line old" data-linenumber="351" 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="LC315" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">sim</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">min</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">similarity</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">additional</span> <span class="nv" style="color: teal;">hits</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">..</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">[</span><span class="nv" style="color: teal;">default:</span> <span class="mf" style="color: #099;">0.95</span><span class="p">]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="316" 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">
316
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">step</span><span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">generate</span> <span class="nv" style="color: teal;">indices</span></span>
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<td class="diff-line-num old old_line" data-linenumber="317" 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">
317
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="perl"> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">run</span> <span class="nv" style="color: teal;">blast</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">and</span> <span class="nv" style="color: teal;">ff</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">adj</span><span class="p">,</span> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">synteny</span> <span class="nv" style="color: teal;">is</span> <span class="nv" style="color: teal;">set</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="318" 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">
318
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<td class="diff-line-num new_line old" data-linenumber="351" 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="LC318" class="line" lang="perl"> <span class="mi" style="color: #099;">3</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">clustering</span></span>
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<td class="diff-line-num old old_line" data-linenumber="319" 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">
319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="perl"> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">-></span> <span class="nv" style="color: teal;">all</span> <span class="p">(</span><span class="nv" style="color: teal;">default</span><span class="p">)</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">nograph</span> <span class="k" style="font-weight: 600;">do</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: teal;">generate</span> <span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">graph</span> <span class="nv" style="color: teal;">file</span> <span class="p">(</span><span class="nv" style="color: teal;">pairwise</span> <span class="nv" style="color: teal;">orthology</span> <span class="nv" style="color: teal;">relations</span><span class="p">)</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="perl"></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: teal;">Misc</span> <span class="nv" style="color: teal;">options</span><span class="p">]</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">desc</span> <span class="nb" style="color: #0086b3;">write</span> <span class="nv" style="color: teal;">description</span> <span class="nv" style="color: teal;">files</span> <span class="p">(</span><span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">NCBI</span> <span class="nv" style="color: teal;">FASTA</span> <span class="nv" style="color: teal;">input</span> <span class="nv" style="color: teal;">only</span><span class="p">)</span></span>
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320
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">blastpath</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">path</span> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">your</span> <span class="nb" style="color: #0086b3;">local</span> <span class="nv" style="color: teal;">blast</span> <span class="p">(</span><span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nv" style="color: teal;">installed</span> <span class="nv" style="color: teal;">globally</span><span class="p">)</span></span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">verbose</span> <span class="nv" style="color: teal;">keeps</span> <span class="nv" style="color: teal;">you</span> <span class="nv" style="color: teal;">informed</span> <span class="nv" style="color: teal;">about</span> <span class="nv" style="color: teal;">the</span> <span class="nv" style="color: teal;">progress</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">clean</span> <span class="nv" style="color: teal;">remove</span> <span class="nv" style="color: teal;">all</span> <span class="nv" style="color: teal;">unnecessary</span> <span class="nv" style="color: teal;">files</span> <span class="nv" style="color: teal;">after</span> <span class="nv" style="color: teal;">processing</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">graph</span> <span class="nv" style="color: teal;">generate</span> <span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">graph</span> <span class="nv" style="color: teal;">files</span> <span class="p">(</span><span class="nv" style="color: teal;">pairwise</span> <span class="nv" style="color: teal;">orthology</span> <span class="nv" style="color: teal;">relations</span><span class="p">)</span></span>
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324
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">debug</span> <span class="nv" style="color: teal;">gives</span> <span class="nv" style="color: teal;">detailed</span> <span class="nv" style="color: teal;">information</span> <span class="k" style="font-weight: 600;">for</span> <span class="nv" style="color: teal;">bug</span> <span class="nv" style="color: teal;">tracking</span></span>
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325
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="perl"> <span class="nv" style="color: teal;">More</span> <span class="nv" style="color: teal;">specific</span> <span class="nv" style="color: teal;">blast</span> <span class="nv" style="color: teal;">parameters</span> <span class="nv" style="color: teal;">can</span> <span class="nv" style="color: teal;">be</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">by</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">blastParameters</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'[parameters]'</span> <span class="p">(</span><span class="nv" style="color: teal;">e</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">g</span><span class="o" style="font-weight: 600;">.</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">blastParameters</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'-seg no'</span><span class="p">)</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="perl"></span>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="perl"> <span class="nv" style="color: teal;">In</span> <span class="k" style="font-weight: 600;">case</span> <span class="nv" style="color: teal;">jobs</span> <span class="nv" style="color: teal;">should</span> <span class="nv" style="color: teal;">be</span> <span class="nv" style="color: teal;">distributed</span> <span class="nv" style="color: teal;">onto</span> <span class="nv" style="color: teal;">several</span> <span class="nv" style="color: teal;">machines</span><span class="p">,</span> <span class="k" style="font-weight: 600;">use</span></span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">startat</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">File</span> <span class="nv" style="color: teal;">number</span> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">start</span> <span class="nv" style="color: teal;">with</span> <span class="p">(</span><span class="nv" style="color: teal;">default:</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">stopat</span><span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">File</span> <span class="nv" style="color: teal;">number</span> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">end</span> <span class="nv" style="color: teal;">with</span> <span class="p">(</span><span class="nv" style="color: teal;">default:</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="perl"></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="perl"> <span class="p">[</span><span class="nv" style="color: teal;">Large</span> <span class="nv" style="color: teal;">compute</span> <span class="nv" style="color: teal;">jobs</span><span class="p">]</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="perl"> <span class="nv" style="color: teal;">In</span> <span class="k" style="font-weight: 600;">case</span> <span class="nv" style="color: teal;">jobs</span> <span class="nv" style="color: teal;">should</span> <span class="nv" style="color: teal;">be</span> <span class="nv" style="color: teal;">distributed</span> <span class="nv" style="color: teal;">onto</span> <span class="nv" style="color: teal;">several</span> <span class="nv" style="color: teal;">machines</span><span class="p">,</span> <span class="k" style="font-weight: 600;">use</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">jobs</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">M</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: teal;">N</span> <span class="nv" style="color: teal;">N</span> <span class="nv" style="color: teal;">defines</span> <span class="nv" style="color: teal;">the</span> <span class="nv" style="color: teal;">number</span> <span class="nv" style="color: teal;">of</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">job</span> <span class="nv" style="color: teal;">groups</span> <span class="p">(</span><span class="nv" style="color: teal;">e</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">g</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">PCs</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="perl"> <span class="nv" style="color: teal;">M</span> <span class="nv" style="color: teal;">defines</span> <span class="nv" style="color: teal;">the</span> <span class="nv" style="color: teal;">set</span> <span class="nv" style="color: teal;">of</span> <span class="nv" style="color: teal;">jobs</span> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">run</span> <span class="nv" style="color: teal;">in</span> <span class="nv" style="color: teal;">this</span> <span class="nv" style="color: teal;">process</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="perl"> <span class="nv" style="color: teal;">Example:</span> <span class="nv" style="color: teal;">run</span> <span class="nv" style="color: teal;">with</span> </span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">step</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="perl"> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">prepare</span> <span class="nv" style="color: teal;">data</span> <span class="k" style="font-weight: 600;">then</span> <span class="nv" style="color: teal;">to</span> <span class="nb" style="color: #0086b3;">split</span> <span class="nv" style="color: teal;">a</span> <span class="nv" style="color: teal;">run</span> <span class="nv" style="color: teal;">on</span> <span class="nv" style="color: teal;">two</span> <span class="nv" style="color: teal;">machines</span> <span class="k" style="font-weight: 600;">use</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">jobs</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">step</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span> <span class="nv" style="color: teal;">on</span> <span class="nv" style="color: teal;">PC</span> <span class="nv" style="color: teal;">one</span> <span class="ow" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">jobs</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">step</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span> <span class="nv" style="color: teal;">on</span> <span class="nv" style="color: teal;">PC</span> <span class="nv" style="color: teal;">two</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="perl"> <span class="nv" style="color: teal;">finally</span> <span class="nv" style="color: teal;">run</span> <span class="nv" style="color: teal;">with</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="perl"> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">step</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span> <span class="nv" style="color: teal;">to</span> <span class="nv" style="color: teal;">finalize</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="perl"><span class="nv" style="color: teal;">JUS</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="perl"></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">@@ -373,7 +410,23 @@ sub set_threads_per_process {</td>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">run_blast</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Jobs todo</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="perl"> <span class="nv" style="color: teal;">$jobs_todo</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$k</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$startat</span><span class="p">;</span> <span class="nv" style="color: teal;">$k</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">);</span> <span class="nv" style="color: teal;">$k</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: teal;">$jobs_todo</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">$k</span><span class="o" style="font-weight: 600;">+</span><span class="nv" style="color: teal;">$selfblast</span><span class="p">;</span><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nv" style="color: teal;">$k</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}}</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nv" style="color: teal;">$selfblast</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: teal;">$jobs_todo</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nv" style="color: teal;">$selfblast</span><span class="p">;}</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Divide 5.16</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="perl"> <span class="nv" style="color: teal;">$part</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: teal;">$jobs_todo</span><span class="o" style="font-weight: 600;">/</span><span class="nv" style="color: teal;">$split_to_X_jobs</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># Round up to not miss anything</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># print STDERR "$jobs_todo/$split_to_X_jobs = $part\n";</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$from</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobnumber</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: teal;">$part</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: teal;">$from</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$to</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobnumber</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: teal;">$part</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="nv" style="color: teal;">$part</span><span class="p">;</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobnumber</span> <span class="o" style="font-weight: 600;">==</span> <span class="nv" style="color: teal;">$split_to_X_jobs</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: teal;">$to</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$jobs_todo</span><span class="p">;}</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="perl"> <span class="nv" style="color: teal;">$part</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nv" style="color: teal;">$to</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">$from</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># real part</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$part</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"I have problems coordinating $split_to_X_jobs groups for $jobs_todo jobs."</span><span class="p">);}</span></span>
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: teal;">$from</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: teal;">$to</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: teal;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="nv" style="color: teal;">$part</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># print STDERR "$from - $to (TODO: $jobs_todo)\n";</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="perl"></span>
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377
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">set_threads_per_process</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># Check if we can apply more threads, nothing is running so far</span></span>
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378
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">print_blast_stats</span><span class="p">();</span></span>
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432
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="perl"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -381,26 +434,26 @@ sub run_blast {</td>
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381
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434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$cpus</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: teal;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">create</span><span class="p">(</span><span class="s" style="color: #d14;">'workerthread'</span><span class="p">);}</span></span>
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435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="perl"></span>
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383
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436
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># For each file against each other file</span></span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$startat</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">);</span> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$job_number</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="perl"> <span class="nv" style="color: teal;">SPEC:</span> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">+</span><span class="nv" style="color: teal;">$selfblast</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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385
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$j</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">$selfblast</span><span class="p">;</span> <span class="nv" style="color: teal;">$j</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">);</span> <span class="nv" style="color: teal;">$j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="perl"> <span class="nv" style="color: teal;">$job_number</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$from</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$job_number</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$from</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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386
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Wait for queque to get empty (with some buffer)</span></span>
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387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobque</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">256</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="nv" style="color: teal;">$cpus</span><span class="p">)</span> <span class="p">{</span></span>
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388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="perl"> <span class="p">}</span></span>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobque</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">pending</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">32</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="nv" style="color: teal;">$cpus</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);}</span></span>
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390
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444
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Syncronize with other processes</span></span>
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391
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="perl"> <span class="nv" style="color: teal;">$jobque</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">enqueue</span><span class="p">(</span><span class="s" style="color: #d14;">"$i $j"</span><span class="p">);</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># print STDERR "EN: $job_number -> $i $j\n";</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$to</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$job_number</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$to</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">last</span> <span class="nv" style="color: teal;">SPEC</span><span class="p">;}</span></span>
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392
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448
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="perl"> <span class="p">}</span></span>
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393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Start-Stop</span></span>
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<td class="diff-line-num old old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$stopat</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nv" style="color: teal;">$i</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span></span>
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395
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449
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="perl"> <span class="p">}</span></span>
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396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="perl"></span>
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397
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450
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Tell all threads they can stop</span></span>
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398
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451
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="perl"> <span class="p">{</span><span class="nv" style="color: teal;">lock</span><span class="p">(</span><span class="nv" style="color: teal;">$all_jobs_submitted</span><span class="p">);</span> <span class="nv" style="color: teal;">$all_jobs_submitted</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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399
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="perl"></span>
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400
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Wait until all jobs are done</span></span>
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401
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="nv" style="color: teal;">threads</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">list</span><span class="p">())</span> <span class="p">{</span><span class="nv" style="color: teal;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nb" style="color: #0086b3;">join</span><span class="p">();}</span></span>
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402
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">print_blast_stats</span><span class="p">();</span> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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403
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">-> Output</span> written to $simgraph\n"</span><span class="p">;</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">[OUTPUT] -></span> written to $simgraph\n"</span><span class="p">;</span></span>
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404
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457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="perl"><span class="p">}</span></span>
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405
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="perl"></span>
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406
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459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">workerthread</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="423" 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="476" 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">@@ -423,7 +476,7 @@ sub workerthread {</td>
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423
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="perl"></span>
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424
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477
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="perl"> <span class="p">{</span></span>
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425
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<td class="diff-line-num new_line" data-linenumber="478" 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">
478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="perl"> <span class="nv" style="color: teal;">lock</span><span class="p">(</span><span class="nv" style="color: teal;">$jobs_done</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># Productive</span></span>
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426
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobs_done</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$jobs_todo</span><span class="p"><span class="idiff left">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff right"> </span> <span class="c1" style="color: #998; font-style: italic;"># Productive</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$jobs_done</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$jobs_todo</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$part</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$jobs_done</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$part</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">{</span></span> <span class="c1" style="color: #998; font-style: italic;"># Productive</span></span>
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># lock($all_jobs_submitted); # DEBUGGING</span></span>
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># if ($all_jobs_submitted) { # DEBUGGING</span></span>
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429
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Thread $thread_id\tis leaving\n"</span><span class="p">;}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="459" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="512" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -459,6 +512,8 @@ sub workerthread {</td>
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459
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512
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="perl"> <span class="nv" style="color: teal;">$result_ji</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">blast</span><span class="p">(</span><span class="nv" style="color: teal;">$file_j</span><span class="p">,</span><span class="nv" style="color: teal;">$file_i</span><span class="p">);</span></span>
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460
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513
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="perl"> <span class="p">}</span></span>
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461
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514
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<pre style="margin: 0;"> <span id="LC514" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$file_i</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: teal;">$file_j</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="nv" style="color: teal;">$selfblast</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Selfblast is disabled but I want to check $file_i vs $file_j"</span><span class="p">);}</span></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="perl"></span>
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462
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%lengths</span><span class="p">;</span></span>
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463
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$file_i</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: teal;">$file_j</span><span class="p">)</span> <span class="p">{</span></span>
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464
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519
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<pre style="margin: 0;"> <span id="LC519" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Get lengths once is enough (selfblast)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="490" 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="545" 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">@@ -490,7 +545,7 @@ sub workerthread {</td>
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490
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%full_id_map_i</span><span class="p">;</span></span>
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491
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%full_id_map_j</span><span class="p">;</span></span>
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492
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%reciprocal_matches</span><span class="p">)</span> <span class="p">{</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">" "</span></span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">);</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;"><span class="idiff left right">/\s/</span></span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">);</span></span>
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494
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$aa</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">convertNCBI</span><span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$bb</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">convertNCBI</span><span class="p">(</span><span class="nv" style="color: teal;">$b</span><span class="p">);</span></span>
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496
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$aa</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nv" style="color: teal;">$a</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -694,13 +749,13 @@ sub synteny_matches {</td>
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694
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749
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<pre style="margin: 0;"> <span id="LC749" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@multis</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># array that contains all multi-edges</span></span>
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695
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750
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<pre style="margin: 0;"> <span id="LC750" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Convert reciprocal matches to ffadj input</span></span>
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696
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%reciprocal_matches</span><span class="p">)</span> <span class="p">{</span></span>
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697
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@values</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">" "</span></span><span class="p">,</span><span class="nv" style="color: teal;">$reciprocal_matches</span><span class="p">{</span><span class="nv" style="color: teal;">$_</span><span class="p">});</span></span>
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698
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">" "</span></span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">);</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@values</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;"><span class="idiff left right">/\s/</span></span><span class="p">,</span><span class="nv" style="color: teal;">$reciprocal_matches</span><span class="p">{</span><span class="nv" style="color: teal;">$_</span><span class="p">});</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;"><span class="idiff left right">/\s/</span></span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">);</span></span>
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699
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754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$order</span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="p">}))</span> <span class="p">{</span><span class="nv" style="color: teal;">$a</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">convertNCBI</span><span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">);}</span></span>
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700
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$order</span><span class="p">{</span><span class="nv" style="color: teal;">$b</span><span class="p">}))</span> <span class="p">{</span><span class="nv" style="color: teal;">$b</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">convertNCBI</span><span class="p">(</span><span class="nv" style="color: teal;">$b</span><span class="p">);}</span></span>
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701
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">" "</span></span><span class="p">,</span><span class="nv" style="color: teal;">$order</span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="p">});</span></span>
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702
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">" "</span></span><span class="p">,</span><span class="nv" style="color: teal;">$order</span><span class="p">{</span><span class="nv" style="color: teal;">$b</span><span class="p">});</span></span>
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703
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">();}</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;"><span class="idiff left right">/\s/</span></span><span class="p">,</span><span class="nv" style="color: teal;">$order</span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="p">});</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;"><span class="idiff left right">/\s/</span></span><span class="p">,</span><span class="nv" style="color: teal;">$order</span><span class="p">{</span><span class="nv" style="color: teal;">$b</span><span class="p">});</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"Failed parsing gene IDs from blast output/gff input\n"</span></span><span class="p">);}</span></span>
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704
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="perl"></span>
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$multis</span><span class="p">[</span><span class="nv" style="color: teal;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]))</span> <span class="p">{</span><span class="nv" style="color: teal;">$multis</span><span class="p">[</span><span class="nv" style="color: teal;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$b</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];}</span></span>
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706
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761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="nv" style="color: teal;">$multis</span><span class="p">[</span><span class="nv" style="color: teal;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">','</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$b</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -765,7 +820,14 @@ sub print_blast_stats {</td>
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765
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="perl"> <span class="nv" style="color: teal;">lock</span><span class="p">(</span><span class="nv" style="color: teal;">$jobs_done</span><span class="p">);</span></span>
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766
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821
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: teal;">$jobs_done</span><span class="sr" style="color: #009926;">/$jobs_todo*10000)/</span><span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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767
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822
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\r "</span><span class="p">;</span></span>
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768
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\rRunning blast analysis: $percent% ($jobs_done/$jobs_todo)"</span><span class="p">;</span></span>
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823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="perl"> </span>
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824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$split_to_X_jobs</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\rRunning blast analysis: $percent% ($jobs_done/$jobs_todo)"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="perl"> <span class="p">}</span></span>
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827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> <span class="c1" style="color: #998; font-style: italic;"># 5.16</span></span>
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828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="perl"> <span class="nv" style="color: teal;">$percent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nv" style="color: teal;">$jobs_done</span><span class="sr" style="color: #009926;">/$part*10000)/</span><span class="mi" style="color: #099;">100</span><span class="p">;</span></span>
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829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"\rRunning blast analysis: $percent% ($jobs_done/$part, $jobs_todo in total)"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="perl"> <span class="p">}</span></span>
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="perl"> <span class="p">}</span></span>
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="perl"><span class="p">}</span></span>
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="perl"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -823,8 +885,10 @@ sub get_legal_matches {</td>
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<pre style="margin: 0;"> <span id="LC885" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"tblastx+"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$blastmode</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"tblastx"</span><span class="p">)</span> <span class="p">{</span><span class="nv" style="color: teal;">$alignment_length</span> <span class="o" style="font-weight: 600;">*=</span> <span class="mi" style="color: #099;">3</span><span class="p">;}</span></span>
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$length</span><span class="p">{</span><span class="nv" style="color: teal;">$query_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: teal;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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825
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$alignment_length</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$length</span><span class="p">{</span><span class="nv" style="color: teal;">$subject_id</span><span class="p">}</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: teal;">$coverage</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">100</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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888
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="perl"></span>
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826
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889
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># It hit itself (only during selfblast)</span></span>
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827
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$query_id</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="nv" style="color: teal;">$subject_id</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># if ($selfblast && $query_id eq $subject_id) {next;} # 5.16 reuse IDs</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">## Listing them in the graph is okay, clustering will ignore them</span></span>
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828
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892
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<pre style="margin: 0;"> <span id="LC892" class="line" lang="perl"></span>
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829
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893
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<pre style="margin: 0;"> <span id="LC893" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Similar hits? Take the better one</span></span>
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830
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894
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$result</span><span class="p">{</span><span class="s" style="color: #d14;">"$query_id $subject_id"</span><span class="p">}))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -844,17 +908,22 @@ sub get_legal_matches {</td>
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844
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Auto set the number of CPUs</span></span>
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845
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">auto_cpus</span> <span class="p">{</span></span>
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846
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$cpus</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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848
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Linux</span></span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">e</span> <span class="s" style="color: #d14;">"/proc/cpuinfo"</span><span class="p">)</span> <span class="p">{</span></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="perl"> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qx(grep processor /proc/cpuinfo | wc -l)</span><span class="p">;</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qx(getconf _NPROCESSORS_ONLN)</span><span class="p">;</span> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[^0-9]//g</span><span class="p">;</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Fallback</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$cpu_x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="914" 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">
914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Linux</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="915" 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">
915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">e</span> <span class="s" style="color: #d14;">"/proc/cpuinfo"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="916" 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">
916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="perl"> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qx(grep processor /proc/cpuinfo | wc -l)</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="917" 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">
917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="918" 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">
918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Try Mac</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="919" 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">
919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="920" 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">
920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="perl"> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qx(system_profiler | grep CPUs:)</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="921" 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">
921
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="851" 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="922" 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">
922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="perl"> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[^0-9]//g</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="851" 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">
851
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<td class="diff-line-num new_line" data-linenumber="923" 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">
923
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="852" 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">
852
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<td class="diff-line-num new_line old" data-linenumber="924" 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="LC852" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Try Mac</span></span>
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<td class="diff-line-num old old_line" data-linenumber="853" 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">
853
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<td class="diff-line-num new_line old" data-linenumber="924" 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="LC853" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="854" 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">
854
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<td class="diff-line-num new_line old" data-linenumber="924" 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="LC854" class="line" lang="perl"> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="sx" style="color: #d14;">qx(system_profiler | grep CPUs:)</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="855" 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="924" 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">
924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$cpu_x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="855" 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="925" 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">
925
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<pre style="margin: 0;">+<span id="LC925" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"failed! Use 1 core only\n"</span><span class="p">;</span><span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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855
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<td class="diff-line-num new_line" data-linenumber="926" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
926
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="856" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
856
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<td class="diff-line-num new_line old" data-linenumber="927" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="perl"> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/[^0-9]//g</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="857" 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">
857
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<td class="diff-line-num new_line old" data-linenumber="927" 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="LC857" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$cpu_x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"failed! Use 1 core only\n"</span><span class="p">;</span><span class="nv" style="color: teal;">$cpu_x</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<td class="diff-line-num old_line" data-linenumber="858" 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">
858
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<td class="diff-line-num new_line" data-linenumber="927" 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">
927
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Detected $cpu_x available CPU threads, "</span><span class="p">;</span></span>
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859
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<td class="diff-line-num new_line" data-linenumber="928" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
928
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="perl"> <span class="nv" style="color: teal;">$cpus</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cpu_x</span><span class="p">;</span></span>
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860
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<td class="diff-line-num new_line" data-linenumber="929" 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">
929
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="892" 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="961" 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">@@ -892,8 +961,9 @@ sub blast {</td>
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892
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961
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<pre style="margin: 0;"> <span id="LC961" class="line" lang="perl"></span>
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893
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962
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># File does not exists yet or I am forced to rewrite it</span></span>
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<td class="diff-line-num old_line" data-linenumber="894" 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">
894
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">s</span> <span class="nv" style="color: teal;">$bla</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$force</span><span class="p">)</span> <span class="p">{</span></span>
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895
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<td class="diff-line-num new_line old" data-linenumber="964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC895" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"$command >$bla\n"</span><span class="p">;}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="896" 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">
896
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<td class="diff-line-num new_line old" data-linenumber="964" 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="LC896" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$command | sort -k11,11g >'$bla'"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># run blast and presort (speeds up best alignment search but is NOT mandatory)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="897" 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="964" 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">
964
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<pre style="margin: 0;">+<span id="LC964" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$debug</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"$command >$bla.tmp\n"</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;"># 5.16</span></span>
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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"$command | sort -k11,11g >'$bla.tmp'"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># run blast and presort (speeds up best alignment search but is NOT mandatory) # 5.16</span></span>
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<td class="diff-line-num new old_line" data-linenumber="897" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
966
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">system</span><span class="p">(</span><span class="s" style="color: #d14;">"mv '$bla.tmp' '$bla'"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># move when done, aids when job fails (no half bla files) # 5.16</span></span>
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897
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<td class="diff-line-num new_line" data-linenumber="967" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
967
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@data</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">readFile</span><span class="p">(</span><span class="nv" style="color: teal;">$bla</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="898" 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">
898
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<td class="diff-line-num new_line" data-linenumber="968" 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">
968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$keep</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">unlink</span><span class="p">(</span><span class="nv" style="color: teal;">$bla</span><span class="p">);}</span> <span class="c1" style="color: #998; font-style: italic;"># delete tmp file</span></span>
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899
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969
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">@data</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="956" 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="1026" 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">@@ -956,11 +1026,12 @@ sub check_blast {</td>
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956
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1026
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<pre style="margin: 0;"> <span id="LC1026" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="957" 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">
957
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<td class="diff-line-num new_line" data-linenumber="1027" 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">
1027
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<pre style="margin: 0;"> <span id="LC1027" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Check plausibility of files</span></span>
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<td class="diff-line-num old_line" data-linenumber="958" 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">
958
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<td class="diff-line-num new_line" data-linenumber="1028" 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">
1028
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<pre style="margin: 0;"> <span id="LC1028" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">check_files</span> <span class="p">{</span></span>
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959
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<td class="diff-line-num new_line old" data-linenumber="1029" 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="LC959" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%ids</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="960" 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">
960
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<td class="diff-line-num new_line" data-linenumber="1029" 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">
1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$step</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">print_usage</span><span class="p">;</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"I need at least two files to compare something!"</span><span class="p">);}</span></span>
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<td class="diff-line-num old_line" data-linenumber="961" 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">
961
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<td class="diff-line-num new_line" data-linenumber="1030" 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">
1030
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Checking input files\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="962" 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">
962
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<td class="diff-line-num new_line" data-linenumber="1031" 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">
1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file</span> <span class="p">(</span><span class="nv" style="color: teal;">@files</span><span class="p">)</span> <span class="p">{</span></span>
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963
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<td class="diff-line-num new_line old" data-linenumber="1032" 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="LC963" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">read_details</span><span class="p">(</span><span class="nv" style="color: teal;">$file</span><span class="p">,</span><span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">%ids</span><span class="p">);</span></span>
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1032
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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Checking $file... "</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1033
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">read_details</span><span class="p">(</span><span class="nv" style="color: teal;">$file</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="964" 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="1034" 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">
1034
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"ok\n"</span><span class="p">;}</span></span>
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964
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<td class="diff-line-num new_line" data-linenumber="1035" 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">
1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="965" 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">
965
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<td class="diff-line-num new_line" data-linenumber="1036" 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">
1036
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<pre style="margin: 0;"> <span id="LC1036" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="966" 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">
966
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<td class="diff-line-num new_line" data-linenumber="1037" 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">
1037
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1037" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="972" 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="1043" 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">@@ -972,12 +1043,13 @@ sub convertNCBI {</td>
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972
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<td class="diff-line-num new_line" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;"> <span id="LC1043" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="973" 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">
973
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<td class="diff-line-num new_line" data-linenumber="1044" 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">
1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="974" 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">
974
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<td class="diff-line-num new_line" data-linenumber="1045" 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">
1045
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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">read_details</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="975" 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">
975
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<td class="diff-line-num new_line old" data-linenumber="1046" 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="LC975" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%ids</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="976" 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="1046" 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">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%ids</span><span class="p">;</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># local test for duplicated IDs</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="976" 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">
976
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<td class="diff-line-num new_line" data-linenumber="1047" 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">
1047
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%genes</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="977" 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">
977
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<td class="diff-line-num new_line" data-linenumber="1048" 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">
1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">shift</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="978" 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">
978
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<td class="diff-line-num new_line" data-linenumber="1049" 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">
1049
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<pre style="margin: 0;"> <span id="LC1049" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$test</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
979
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<td class="diff-line-num new_line old" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC979" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span><span class="nv" style="color: teal;">$test</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="idiff left"> </span><span class="nv" style="color: teal;"><span class="idiff">%ids</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">%</span></span><span class="p"><span class="idiff">{(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">shift</span></span><span class="p"><span class="idiff right">)};</span>}</span> <span class="c1" style="color: #998; font-style: italic;"># if no ID Hash is give, we do not want to test but to fetch the gff data</span></span>
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<td class="diff-line-num new old_line" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1050
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<pre style="margin: 0;">+<span id="LC1050" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span><span class="nv" style="color: teal;">$test</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;"># if no ID Hash is give, we do not want to test but to fetch the gff data</span></span>
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<td class="diff-line-num old_line" data-linenumber="980" 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">
980
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<td class="diff-line-num new_line" data-linenumber="1051" 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">
1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="perl"></span>
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<td class="diff-line-num new old_line" data-linenumber="981" 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="1052" 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">
1052
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<pre style="margin: 0;">+<span id="LC1052" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># print STDERR "TEST: $test\n";</span></span>
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<td class="diff-line-num old_line" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
981
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<td class="diff-line-num new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!-</span><span class="nv" style="color: teal;">e</span> <span class="nv" style="color: teal;">$file</span><span class="p">)</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"File '$file' not found!"</span><span class="p">);}</span></span>
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<td class="diff-line-num old_line" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
982
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<td class="diff-line-num new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1054
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<pre style="margin: 0;"> <span id="LC1054" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">FASTA</span><span class="p">,</span><span class="s" style="color: #d14;">"<$file"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not open '$file': $!"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="983" 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">
983
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><FASTA></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="987" 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="1059" 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">@@ -987,7 +1059,8 @@ sub read_details {</td>
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<td class="diff-line-num old_line" data-linenumber="987" 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">
987
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<td class="diff-line-num new_line" data-linenumber="1059" 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">
1059
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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="perl"> <span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^>//</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="988" 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">
988
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<td class="diff-line-num new_line" data-linenumber="1060" 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">
1060
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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="perl"> <span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/\s.*//</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
989
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<td class="diff-line-num new_line" data-linenumber="1061" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1061
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<pre style="margin: 0;"> <span id="LC1061" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$test</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="990" 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">
990
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<td class="diff-line-num new_line old" data-linenumber="1062" 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="LC990" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$ids</span><span class="p">{</span><span class="nv" style="color: teal;">$_</span><span class="p">}))</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Gene ID '$_' is defined at least twice:\n$ids{$_}\n$file"</span><span class="p">);}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="991" 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="1062" 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">
1062
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<pre style="margin: 0;">+<span id="LC1062" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># print STDERR "ID: $_\n";</span></span>
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<td class="diff-line-num new old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1063" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1063
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<pre style="margin: 0;">+<span id="LC1063" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$ids</span><span class="p">{</span><span class="nv" style="color: teal;">$_</span><span class="p">}))</span> <span class="p">{</span><span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Gene ID '$_' is defined at least twice in $file"</span><span class="p">);}</span></span>
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<td class="diff-line-num old_line" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
991
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<td class="diff-line-num new_line" data-linenumber="1064" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="perl"> <span class="nv" style="color: teal;">$ids</span><span class="p">{</span><span class="nv" style="color: teal;">$_</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$file</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="992" 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">
992
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<td class="diff-line-num new_line" data-linenumber="1065" 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">
1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="993" 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">
993
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<td class="diff-line-num new_line" data-linenumber="1066" 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">
1066
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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$synteny</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1001,10 +1074,11 @@ sub read_details {</td>
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<td class="diff-line-num old_line" data-linenumber="1001" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1001
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<td class="diff-line-num new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1074
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<pre style="margin: 0;"> <span id="LC1074" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$synteny</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span><span class="p">;}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1002" 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">
1002
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<td class="diff-line-num new_line" data-linenumber="1075" 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">
1075
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<pre style="margin: 0;"> <span id="LC1075" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1003" 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">
1003
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<td class="diff-line-num new_line" data-linenumber="1076" 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">
1076
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<pre style="margin: 0;"> <span id="LC1076" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%coordinates</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1004" 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">
1004
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<td class="diff-line-num new_line old" data-linenumber="1077" 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="LC1004" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$test</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"$file\t"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%genes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">" genes\<span class="idiff left right">n</span>"</span><span class="p">;}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1005" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$test</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"$file\t"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%genes</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">" genes\<span class="idiff left right">t</span>"</span><span class="p">;}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1005" 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">
1005
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<td class="diff-line-num new_line" data-linenumber="1078" 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">
1078
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<pre style="margin: 0;"> <span id="LC1078" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$gff</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">gff4fasta</span><span class="p">(</span><span class="nv" style="color: teal;">$file</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1006" 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">
1006
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<td class="diff-line-num new_line" data-linenumber="1079" 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">
1079
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<pre style="margin: 0;"> <span id="LC1079" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">GFF</span><span class="p">,</span><span class="s" style="color: #d14;">"<$gff"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not open '$gff': $!"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1007
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<td class="diff-line-num new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1080
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<pre style="margin: 0;"> <span id="LC1080" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><GFF></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^##FASTA/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">last</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;"># deal with prokka gffs, thx 2 Ben Woodcroft</span></span>
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<td class="diff-line-num old_line" data-linenumber="1008" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1008
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<td class="diff-line-num new_line" data-linenumber="1082" 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">
1082
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<pre style="margin: 0;"> <span id="LC1082" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^#/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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1009
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1083
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<pre style="margin: 0;"> <span id="LC1083" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># e.g. NC_009925.1 RefSeq CDS 9275 10096 . - 0 ID=cds8;Name=YP_001514414.1;Parent=gene9;Dbxref=Genbank:YP_001514414.1,GeneID:5678848;gbkey=CDS;product=signal peptide peptidase SppA;protein_id=YP_001514414.1;transl_table=11</span></span>
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1010
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<td class="diff-line-num new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1084
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<pre style="margin: 0;"> <span id="LC1084" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@col</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t+/</span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1033" 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="1107" 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">@@ -1033,7 +1107,7 @@ sub read_details {</td>
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1033
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1107
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<pre style="margin: 0;"> <span id="LC1107" class="line" lang="perl"><span class="p">}</span></span>
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1034
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1108
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<pre style="margin: 0;"> <span id="LC1108" class="line" lang="perl"></span>
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1035
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<td class="diff-line-num new_line" data-linenumber="1109" 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">
1109
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<pre style="margin: 0;"> <span id="LC1109" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">Error</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1036" 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">
1036
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<td class="diff-line-num new_line old" data-linenumber="1110" 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="LC1036" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">Error:</span> "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1110
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<pre style="margin: 0;">+<span id="LC1110" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">\n[ERROR]</span> "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$_</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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1037
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1111
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<pre style="margin: 0;"> <span id="LC1111" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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1038
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1112
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<pre style="margin: 0;"> <span id="LC1112" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1039" 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">
1039
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<td class="diff-line-num new_line" data-linenumber="1113" 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">
1113
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<pre style="margin: 0;"> <span id="LC1113" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1075" 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="1149" 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">@@ -1075,6 +1149,6 @@ sub write_descriptions {</td>
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1075
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1149
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<pre style="margin: 0;"> <span id="LC1149" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1076" 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">
1076
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<td class="diff-line-num new_line" data-linenumber="1150" 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">
1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="perl"> <span class="p">}</span></span>
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1077
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<td class="diff-line-num new_line" data-linenumber="1151" 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">
1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="perl"> <span class="p">}</span></span>
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1078
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<pre style="margin: 0;">-<span id="LC1078" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">-> Output</span> written to $desctable\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1079" 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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1152
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<pre style="margin: 0;">+<span id="LC1152" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"<span class="idiff left right">[OUTPUT] -></span> written to $desctable\n"</span><span class="p">;</span></span>
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1079
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1153
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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="perl"></span>
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1080
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1154
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="perl"><span class="p">}</span></span></pre>
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<li id="63ca7a8ee3bc533f40d25b4b217452dd3d054ed9">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#63ca7a8ee3bc533f40d25b4b217452dd3d054ed9"><strong>proteinortho5_clean_edges2.pl</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,13 +11,19 @@ if (!defined($ARGV[1])) {</td>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Proteinortho Output</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Cleaning edge list...\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Reading removal list</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%map</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">IN</span><span class="p">,</span><span class="s" style="color: #d14;">"<$ARGV[0]"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not open file $ARGV[0]: $!"</span><span class="p">);</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><IN></span><span class="p">)</span> <span class="p">{</span></span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Line does not match filter list pattern\n"</span><span class="p">);}</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$ta</span><span class="p">,</span> <span class="nv" style="color: teal;">$sa</span><span class="p">,</span> <span class="nv" style="color: teal;">$tb</span><span class="p">,</span> <span class="nv" style="color: teal;">$sb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">4</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># name, species, name, species</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$sb</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Line does not match filter list pattern\n"</span><span class="p">);}</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"> <span class="nv" style="color: teal;">$ta</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$sa</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"> <span class="nv" style="color: teal;">$tb</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$sb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span><span class="p">(</span><span class="nv" style="color: teal;">$ta</span><span class="p">,</span><span class="nv" style="color: teal;">$tb</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># bidirectional edges store once is fine</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="perl"> <span class="nv" style="color: teal;">$map</span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$b</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"> </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">IN</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="31" 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">@@ -25,20 +31,48 @@ close(IN);</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="nb" style="color: #0086b3;">shift</span><span class="p">(</span><span class="nv" style="color: teal;">@ARGV</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rm</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$all</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># For all blastgraphs</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$filea</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fileb</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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28
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file</span> <span class="p">(</span><span class="nv" style="color: teal;">@ARGV</span><span class="p">)</span> <span class="p">{</span></span>
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29
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">IN</span><span class="p">,</span><span class="s" style="color: #d14;">"<$file"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not open file $file: $!"</span><span class="p">);</span></span>
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30
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><IN></span><span class="p">)</span> <span class="p">{</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^#/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span><span class="nv" style="color: teal;">$b</span><span class="p">,</span><span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Line does not match Proteinortho graph format\n"</span><span class="p">);}</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="perl"> <span class="nv" style="color: teal;">$all</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span><span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span><span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">);</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="perl"></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: teal;">$map</span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$b</span><span class="p">}))</span> <span class="p">{</span><span class="nv" style="color: teal;">$rm</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span> <span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^#/</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"> <span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/^#\s*//</span><span class="p">;</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span><span class="nv" style="color: teal;">$b</span><span class="p">,</span><span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"a"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$a</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"file_a"</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$b</span><span class="p">))</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Line does not match Proteinortho graph format. Filename missing.\n"</span><span class="p">);}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Keep track of files/species</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"> <span class="nv" style="color: teal;">$filea</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$a</span><span class="p">;</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"> <span class="nv" style="color: teal;">$fileb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$b</span><span class="p">;</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\t/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$ta</span><span class="p">,</span><span class="nv" style="color: teal;">$tb</span><span class="p">,</span><span class="nb" style="color: #0086b3;">undef</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"\t"</span><span class="p">,</span><span class="nv" style="color: teal;">$_</span><span class="p">,</span><span class="mi" style="color: #099;">3</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" 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">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$tb</span><span class="p">)</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="s" style="color: #d14;">"Line does not match Proteinortho graph format\n"</span><span class="p">);}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"> <span class="nv" style="color: teal;">$all</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"> </span>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"> <span class="nv" style="color: teal;">$ta</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$filea</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"> <span class="nv" style="color: teal;">$tb</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">" "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$fileb</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span><span class="p">(</span><span class="nv" style="color: teal;">$ta</span><span class="p">,</span><span class="nv" style="color: teal;">$tb</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;"># bidirectional edges store once is fine</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span><span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sort</span><span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span> <span class="nv" style="color: teal;">$b</span><span class="p">);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">exists</span><span class="p">(</span><span class="nv" style="color: teal;">$map</span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$b</span><span class="p">}))</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="perl"> <span class="nv" style="color: teal;">$rm</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"> <span class="k" style="font-weight: 600;">next</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="perl"> </span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># if ($a eq $b) {$all--; next;} # Selfhits are ignored</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"> <span class="p">}</span></span>
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39
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="perl"> <span class="p">}</span></span>
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40
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">IN</span><span class="p">);</span></span>
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41
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"><span class="p">}</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="perl"></span>
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43
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Removed $rm / $all edges\n"</span><span class="p">;</span></span>
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44
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Done.\n"</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">## TODO: Adjust to remove selfblast hits and watch</span></span></pre>
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<li id="d7b44f60b1891297da292f87114cb80f89d8526f">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#d7b44f60b1891297da292f87114cb80f89d8526f"><strong>proteinortho5_clustering.cpp</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,7 +3,7 @@</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Reads edge list and splits connected components</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * according to algebraic connectivity threshold</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> *</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Last updated: 201<span class="idiff left right">6/04/22</span> </span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Last updated: 201<span class="idiff left right">7/03/20</span> </span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * Author: Marcus Lechner</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"></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">@@ -40,6 +40,8 @@ vector<unsigned int> get_deg_one (vector<unsigned int>& );</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Parameters</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">param_verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">param_con_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">param_sep_purity</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.75</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">param_rmgraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"remove.graph"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// min number of alg con iterations</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">10000</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// max number of alg con iterations</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">@@ -98,6 +100,14 @@ int main(int argc, char *argv[]) {</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cpp"> <span class="n" style="color: #333;">paras</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cpp"> <span class="n" style="color: #333;">param_con_threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string2double</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">paras</span><span class="p">]));</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-purity"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="n" style="color: #333;">paras</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="n" style="color: #333;">param_sep_purity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string2double</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">paras</span><span class="p">]));</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cpp"> <span class="p">}</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-debug"</span><span class="p">)</span> <span class="p">{</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">paras</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">=</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">string2double</span><span class="p">(</span><span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">paras</span><span class="p">])));</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">parameter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-rmgraph"</span><span class="p">)</span> <span class="p">{</span></span>
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102
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="n" style="color: #333;">paras</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">param_rmgraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">string</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">paras</span><span class="p">]);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,9 +119,14 @@ int main(int argc, char *argv[]) {</td>
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109
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"> </span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Debug level "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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112
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp"></span>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parse files</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="p">;</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">parse_file</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">()</span> <span class="p">;</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Parsing file "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" 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">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">parse_file</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" 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">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] I know "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">species_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" species with "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">protein_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" proteins and "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">edges</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" edges in sum"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="p">};</span></span>
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="cpp"></span>
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116
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Free memory</span></span>
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="cpp"> <span class="n" style="color: #333;">files</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="137" 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">@@ -122,6 +137,7 @@ int main(int argc, char *argv[]) {</td>
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122
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<td class="diff-line-num new_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">param_verbose</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">species_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" species"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">protein_counter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" paired proteins"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">edges</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" bidirectional edges"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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123
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138
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="124" 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">
124
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<td class="diff-line-num new_line" data-linenumber="139" 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">
139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Prepare sort of output</span></span>
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<td class="diff-line-num new old_line" data-linenumber="125" 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="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Sorting known species"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="125" 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">
125
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<td class="diff-line-num new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cpp"> <span class="n" style="color: #333;">sort_species</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="126" 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">
126
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
127
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143
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write output header</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="131" 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="147" 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">@@ -131,6 +147,7 @@ int main(int argc, char *argv[]) {</td>
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131
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">graph_clean</span><span class="p">.</span><span class="n" style="color: #333;">open</span><span class="p">(</span><span class="n" style="color: #333;">param_rmgraph</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="132" 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">
132
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148
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"></span>
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133
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Clustering</span></span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Clustering"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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134
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"> <span class="n" style="color: #333;">partition_graph</span><span class="p">();</span></span>
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135
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"> <span class="n" style="color: #333;">graph_clean</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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136
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="283" 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="300" 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">@@ -283,14 +300,19 @@ void partition_graph() {</td>
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283
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="cpp"></span>
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284
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Do not report singles</span></span>
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285
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">current_group</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="286" 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="303" 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">
303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Single gene skipped"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
</pre>
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286
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304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"> <span class="n" style="color: #333;">protein_id</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="287" 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">
287
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305
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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288
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="cpp"> <span class="p">}</span></span>
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289
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="cpp"></span>
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290
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Connectivity analysis</span></span>
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<td class="diff-line-num new new_line" data-linenumber="309" 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">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Calculating connectivity of a group. "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">current_group</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" proteins (ID: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">protein_id</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">")"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">current_group</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">16000</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[WARN] Current connected component conatins "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">current_group</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" proteins. That might be way to much for me. Try raising the e-value!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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291
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">connectivity</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getConnectivity</span><span class="p">(</span><span class="n" style="color: #333;">current_group</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Connectivity was "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">connectivity</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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292
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"></span>
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293
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">connectivity</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">param_con_threshold</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">current_group</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" 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">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] Reiterating"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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294
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Split groups is done in getConnectivity function</span></span>
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295
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Reset flags and repeat without incrementing protein counter</span></span>
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296
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">current_group</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="n" style="color: #333;">done</span><span class="p">[</span><span class="n" style="color: #333;">current_group</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="432" 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="454" 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">@@ -432,7 +454,8 @@ void removeExternalEdges(map<unsigned int,bool>& a) {</td>
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432
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">ita</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">protein</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">ita</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">protein</span><span class="p">].</span><span class="n" style="color: #333;">edges</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">ita</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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433
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If it is not present the own group, set flag</span></span>
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434
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ita</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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435
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">graph_clean</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">protein</span><span class="p">].</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ita</span> <span class="p">].</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Improved graph cleaning</span></span>
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.16 store name AND species in removal list</span></span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="cpp"> <span class="n" style="color: #333;">graph_clean</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">protein</span><span class="p">].</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">species</span><span class="p">[</span><span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="n" style="color: #333;">protein</span><span class="p">].</span><span class="n" style="color: #333;">species_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ita</span> <span class="p">].</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">species</span><span class="p">[</span><span class="n" style="color: #333;">graph</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ita</span> <span class="p">].</span><span class="n" style="color: #333;">species_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Improved graph cleaning</span></span>
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"> <span class="n" style="color: #333;">swap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Otherwise, add it to the new edge list</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="497" 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">@@ -497,12 +520,16 @@ void splitGroups(vector<double>& y, vector<unsigned int>& nodes){</td>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// return;</span></span>
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<pre style="margin: 0;"> <span id="LC521" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// }</span></span>
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<pre style="margin: 0;"> <span id="LC522" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Store data about two groups</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">groupA</span><span class="p">,</span> <span class="n" style="color: #333;">groupB</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Store data about two groups<span class="idiff left right"> (Zero cannot be assigned with certainty)</span></span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">groupA</span><span class="p">,</span> <span class="n" style="color: #333;">groupB</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">groupZero</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">y</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cerr << i << " = " << y[i] << endl; </span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">groupA</span><span class="p">[</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// cerr << graph[nodes[i]].full_name << " {color:#95cde5}" << endl; }</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="n" style="color: #333;">groupB</span><span class="p">[</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// cerr << graph[nodes[i]].full_name << " {color:#b01700}" << endl; }</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="528" 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">
528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">param_sep_purity</span><span class="p">)</span> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="529" 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">
529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG L3] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" = "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -> "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">style</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="530" 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">
530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">param_sep_purity</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">groupZero</span><span class="p">[</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// cerr << graph[nodes[i]].full_name << " {color:#95cde5}" << endl; }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="531" 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">
531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">y</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="n" style="color: #333;">groupA</span><span class="p">[</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// cerr << graph[nodes[i]].full_name << " {color:#95cde5}" << endl; }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="532" 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">
532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="n" style="color: #333;">groupB</span><span class="p">[</span><span class="n" style="color: #333;">nodes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;}</span> <span class="c1" style="color: #998; font-style: italic;">// cerr << graph[nodes[i]].full_name << " {color:#b01700}" << endl; }</span></span>
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506
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="p">}</span></span>
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507
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534
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<pre style="margin: 0;"> <span id="LC534" class="line" lang="cpp"></span>
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508
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535
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<pre style="margin: 0;"> <span id="LC535" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cerr << groupA.size() << " -- " << groupB.size() << endl;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="512" 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="539" 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">@@ -512,22 +539,18 @@ void splitGroups(vector<double>& y, vector<unsigned int>& nodes){</td>
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512
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539
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="s" style="color: #d14;">"Failed to partition subgraph! This might lead to an infinit loop. Please submit the .blastgraph file to lechner@staff.uni-marburg.de to help fixing this issue."</span><span class="p">;</span></span>
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513
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="cpp"> <span class="p">}</span></span>
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514
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="cpp"></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <span class="n" style="color: #333;">removeExternalEdges</span><span class="p">(</span><span class="n" style="color: #333;">groupZero</span><span class="p">);</span></span>
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515
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="cpp"> <span class="n" style="color: #333;">removeExternalEdges</span><span class="p">(</span><span class="n" style="color: #333;">groupA</span><span class="p">);</span></span>
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516
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544
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<pre style="margin: 0;"> <span id="LC544" class="line" lang="cpp"> <span class="n" style="color: #333;">removeExternalEdges</span><span class="p">(</span><span class="n" style="color: #333;">groupB</span><span class="p">);</span></span>
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517
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545
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="cpp"><span class="p">}</span></span>
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518
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546
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="cpp"></span>
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519
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547
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getConnectivity</span><span class="p">(</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">nodes</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Special cases hotfix</span></span>
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<pre style="margin: 0;">-<span id="LC521" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">min</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_deg_one</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fully connected</span></span>
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">min</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;}</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// not</span></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">3</span><span class="p">;}</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Special case quicky</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG L2] Shortcut for two-piece component -> conn = 1"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">Hotfix</span> end</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">quicky</span> end</span></span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get max degree of nodes</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">max_degree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_deg</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -546,7 +569,9 @@ double getConnectivity(vector<unsigned int>& nodes) {</td>
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Repeat until difference < epsilon</span></span>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// catch huge clustering issues by keeping track here</span></span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">++</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">max_iter</span><span class="p">)</span> <span class="p">{</span> </span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">%</span><span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG L2] Step "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" / "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">max_iter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">last_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">current_length</span><span class="p">;</span></span>
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get a new x</span></span>
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552
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577
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="cpp"> <span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_new_x</span><span class="p">(</span><span class="n" style="color: #333;">norm</span><span class="p">,</span> <span class="n" style="color: #333;">nodes</span><span class="p">,</span> <span class="n" style="color: #333;">mapping</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="557" 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="582" 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">@@ -557,9 +582,10 @@ double getConnectivity(vector<unsigned int>& nodes) {</td>
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Get lenght (lambda) & normalize vector</span></span>
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558
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583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">norm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nomalize</span><span class="p">(</span><span class="n" style="color: #333;">x_hat</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">current_length</span><span class="p">);</span></span>
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559
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584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">/// cerr << "I " << iter << ": " << abs(current_length-last_length) << endl; </span></span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">current_length</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">last_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.000<span class="idiff left right">0</span>1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_iter</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// min 100 iterations (prevent convergence by chance), converge to 1e-6</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">current_length</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">last_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0001</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_iter</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// min 100 iterations (prevent convergence by chance), converge to 1e-6</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="cpp"> <span class="p">}</span></span>
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587
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">/// cerr << nodes.size() << " nodes done after " << iter << " iterations" << endl;</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">debug_level</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"[DEBUG] "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" / "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">max_iter</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" iterations required (error is "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">abs</span><span class="p">(</span><span class="n" style="color: #333;">current_length</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">last_length</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">")"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">connectivity</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">current_length</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">max_degree</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">nodes</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"></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">@@ -622,13 +648,13 @@ void parse_file(string file) {</td>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">file_a</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"file_a"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">file_b</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"file_b"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Init Header</span></span>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC625" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Map species a</span></span>
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Map species a<span class="idiff left right"> if not know so far</span></span></span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">species2id</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">file_a</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">species2id</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp"> <span class="n" style="color: #333;">species</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">file_a</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cerr << "Species " << species_counter << ": " << file_a << endl;</span></span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp"> <span class="n" style="color: #333;">species2id</span><span class="p">[</span><span class="n" style="color: #333;">file_a</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">species_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Map species b</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Map species b<span class="idiff left right"> if not know so far</span></span></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">species2id</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">file_b</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">species2id</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cerr << "Species " << species_counter << ": " << file_b << endl;</span></span>
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<pre style="margin: 0;"> <span id="LC660" class="line" lang="cpp"> <span class="n" style="color: #333;">species</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">file_b</span><span class="p">);</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -644,17 +670,27 @@ void parse_file(string file) {</td>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// cerr << protein_counter << ": " << fields[0] << " <-> " << fields[1] << endl;</span></span>
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<pre style="margin: 0;"> <span id="LC672" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.16 deal with duplicated IDs by adding file ID to protein ID</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">ida</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">idb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">file_a_id</span><span class="p">;</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" "</span><span class="p">;</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">file_b_id</span><span class="p">;</span></span>
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678
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 5.16 do not point to yourself</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">compare</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]))</span> <span class="p">{</span><span class="k" style="font-weight: 600;">continue</span><span class="p">;}</span></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// A new protein</span></span>
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<pre style="margin: 0;"> <span id="LC683" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">protein2id</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">protein2id</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp"> <span class="n" style="color: #333;">protein</span> <span class="n" style="color: #333;">a</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC650" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">fields</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">ida</span></span><span class="p">;</span></span>
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686
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="cpp"> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">species_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_a_id</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">protein2id</span><span class="p">[</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protein_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">protein2id</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">protein2id</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="cpp"> <span class="n" style="color: #333;">protein</span> <span class="n" style="color: #333;">b</span><span class="p">;</span></span>
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657
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<pre style="margin: 0;">-<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">species_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_b_id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">full_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">idb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">species_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_b_id</span><span class="p">;</span></span>
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694
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"> <span class="n" style="color: #333;">protein2id</span><span class="p">[</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">protein_counter</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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695
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<pre style="margin: 0;"> <span id="LC695" class="line" lang="cpp"> <span class="n" style="color: #333;">graph</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC696" class="line" lang="cpp"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#b449ded4202264f363300e737ee12e8592179216"><strong>test/C.faa</strong></a>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#a11f8424ded8665fc5fda5e453ed096f53c16922"><strong>test/E.faa</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">@@ -477,14 +477,6 @@ GRNCKAADQPGILTHNKMCQCGDFGLPHEKYGFAHLSRSSFGVSCTACSNPTIVSALHRA</td>
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477
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="plaintext">ESIHRSGAWLNSQDSTETGTNLFGPTSKESRESICGNQFSVTATIGQLGYVTDVLAHGMV</span>
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478
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="plaintext">LAFCDFAKTASAGPPKEKVNCDDGHGGLMLEANVFSEESDVRKHLGLSEKGYHCVLTSKT</span>
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479
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="plaintext">LVKFLIKNQTFHCGAEGCVPTGSGAFGD</span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="plaintext">>L_7</span>
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481
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="plaintext">KEDAIRWPQLGGVSLYGEDANMELGADGVPSTSALGMPWPVLFNANLSGKQCAQCRIFIV</span>
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<pre style="margin: 0;">-<span id="LC482" class="line" lang="plaintext">CHLTQPHFVGAMQVGMSGDDELKDQVKLNGGACKDEFRGNRTLMAMYPFARVLFATPSTV</span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="plaintext">SFDKFILKEGFGFLGRCAAKVAATAPLNGVTTACPVQVVSKCCNKGKKELEPLFTAREHA</span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="plaintext">ADGCGYASAFTVALEKDSYHCDYYSDHAQYASKSYAKSSRALASYFLIQFISCTKGLCSE</span>
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485
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="plaintext">SHECVKNEFLVKIWPGSKMGASIPTNYVMLSDPAYPYECDDHQNNHCSGEKMPKLQNHPG</span>
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486
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="plaintext">YSAFTQRQKSFTKHLTPAKGERKFDMNGVHLDIGKVTPTTSDEYVEALSLVHPTALNPAF</span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="plaintext">GMKAIYYLKRAYKKGLFGLDVHVSKNNTEASKKDYHVVT</span>
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488
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480
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<pre style="margin: 0;"> <span id="LC480" class="line" lang="plaintext">>L_8</span>
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489
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="plaintext">CRLPGGVNERAFGHVNDKDLCMLPSPVFCTQKGKEHPPNKEYQMAGSKPPTWPAAQVVDC</span>
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490
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482
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="plaintext">RHELRTYTGQLPMRSATDLGPNVKSIYTVSERGFKVGQTNHAVCFEAGNVEDKKWKMCHG</span>
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<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#b4cb7401cf06d8f9e64d61ef65084716166606cb"><strong>tools/check_graph_duplicate_ids.pl</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">warnings</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%genehash</span><span class="p">;</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Usage: remove_graph_duplicates.pl <GRAPH\n\nChecks a given graph input for duplicates and removes them (species only)\nReads from STDIN\n"</span><span class="p">;</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">;</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="p">}</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$a</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"unk"</span><span class="p">;</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$b</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"unk"</span><span class="p">;</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><STDIN></span><span class="p">)</span> <span class="p">{</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@row</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^#/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">();}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"file_a"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"a"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"> <span class="nv" style="color: teal;">$a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"> <span class="nv" style="color: teal;">$b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"> <span class="p">}</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># print "$a: $row[0]\n$b: $row[1]\n";</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$genehash</span><span class="p">{</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}))</span> <span class="p">{</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$genehash</span><span class="p">{</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nv" style="color: teal;">$a</span><span class="p">)</span> <span class="p">{</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$row[0] was used with $genehash{$row[0]} and $a\n"</span><span class="p">;</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"> <span class="p">}</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"> <span class="p">}</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"> <span class="nv" style="color: teal;">$genehash</span><span class="p">{</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$a</span><span class="p">;</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"> <span class="p">}</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$genehash</span><span class="p">{</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}))</span> <span class="p">{</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$genehash</span><span class="p">{</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nv" style="color: teal;">$b</span><span class="p">)</span> <span class="p">{</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$row[1] was used with $genehash{$row[1]} and $b\n"</span><span class="p">;</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"> <span class="p">}</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"> <span class="p">}</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"> <span class="nv" style="color: teal;">$genehash</span><span class="p">{</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$b</span><span class="p">;</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"> <span class="p">}</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"> <span class="p">}</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"><span class="p">}</span></span></pre>
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<li id="8311c5e5a1bdf4fa9564aa34ede64baef98d0ebb">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#8311c5e5a1bdf4fa9564aa34ede64baef98d0ebb"><strong>tools/extract_from_graph.pl</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">warnings</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Usage: extract_from_graph.pl PROTEINORTHO_TABLE <GRAPH\n\nExtracts an orthology group from a given graph (STDIN)\n"</span><span class="p">;</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="p">}</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%use_gene</span><span class="p">;</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@species</span><span class="p">;</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">PO</span><span class="p">,</span><span class="s" style="color: #d14;">"<$ARGV[0]"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span><span class="p">(</span><span class="vg" style="color: teal;">$!</span><span class="p">);</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><PO></span><span class="p">)</span> <span class="p">{</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@list</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\t+/</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$list</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"# Species"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"> <span class="nv" style="color: teal;">@species</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@list</span><span class="p">;</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@species</span><span class="p">;</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@species</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@species</span><span class="p">;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@list</span><span class="p">;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@list</span><span class="p">;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">shift</span> <span class="nv" style="color: teal;">@list</span><span class="p">;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nv" style="color: teal;">@list</span><span class="p">);</span> <span class="nv" style="color: teal;">$i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$gene</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">,</span><span class="nv" style="color: teal;">$list</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">]))</span> <span class="p">{</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$gene</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$species</span><span class="p">[</span><span class="nv" style="color: teal;">$i</span><span class="p">];</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"> <span class="nv" style="color: teal;">$use_gene</span><span class="p">{</span><span class="nv" style="color: teal;">$id</span><span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"> <span class="p">}</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"> <span class="p">}</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"> <span class="p">}</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"><span class="p">}</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="perl"><span class="nb" style="color: #0086b3;">close</span><span class="p">(</span><span class="nv" style="color: teal;">PO</span><span class="p">);</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="perl"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="nb" style="color: #0086b3;">scalar</span><span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%use_gene</span><span class="p">);</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">" genes found\n"</span><span class="p">;</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="perl"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file_a</span><span class="p">;</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file_b</span><span class="p">;</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><STDIN></span><span class="p">)</span> <span class="p">{</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^#/</span><span class="p">)</span> <span class="p">{</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@row</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">();}</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"file_a"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"a"</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="perl"> <span class="nv" style="color: teal;">$file_a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="perl"> <span class="nv" style="color: teal;">$file_b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="perl"> <span class="p">}</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="perl"> <span class="p">}</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="perl"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@row</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="55" 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">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ida</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$file_a</span><span class="p">;</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$idb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$file_b</span><span class="p">;</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$use_gene</span><span class="p">{</span><span class="nv" style="color: teal;">$ida</span><span class="p">}</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$use_gene</span><span class="p">{</span><span class="nv" style="color: teal;">$idb</span><span class="p">})</span> <span class="p">{</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"> <span class="p">}</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"> <span class="p">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"><span class="p">}</span></span></pre>
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<li id="ae7905f5a47b30d2a6e01ba97d24279fccbe00a8">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#ae7905f5a47b30d2a6e01ba97d24279fccbe00a8"><strong>tools/graph_conv.pl</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">warnings</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"graph G {\n"</span><span class="p">;</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><STDIN></span><span class="p">)</span> <span class="p">{</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/#/</span><span class="p">)</span> <span class="p">{</span><span class="k" style="font-weight: 600;">next</span><span class="p">;}</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@x</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s/</span><span class="p">);</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">" $x[0] -- $x[1];\n"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"> <span class="p">}</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="p">}</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">" }"</span><span class="p">;</span></span></pre>
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<li id="c507b662cb6847893f5814acc9789d0eb0b960c2">
<a href="https://salsa.debian.org/med-team/proteinortho/commit/6ecf7dce0bb2fb4706bc16e7989b138f814daab2#c507b662cb6847893f5814acc9789d0eb0b960c2"><strong>tools/remove_graph_duplicates.pl</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/perl</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">warnings</span><span class="p">;</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">%filehash</span><span class="p">;</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$flag</span><span class="p">;</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="perl"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">defined</span><span class="p">(</span><span class="nv" style="color: teal;">$ARGV</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]))</span> <span class="p">{</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Usage: remove_graph_duplicates.pl <GRAPH\n\nChecks a given graph input for duplicates and removes them (species only)\nReads from STDIN\n"</span><span class="p">;</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">exit</span><span class="p">;</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="p">}</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="perl"><span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="sr" style="color: #009926;"><STDIN></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$_</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^#/</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="perl"> <span class="nv" style="color: teal;">$flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@row</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">split</span><span class="p">(</span><span class="sr" style="color: #009926;">/\s+/</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">die</span><span class="p">();}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="perl"> <span class="k" style="font-weight: 600;">unless</span> <span class="p">(</span><span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"file_a"</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"a"</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$a</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$row</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$id</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">join</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="p">,</span><span class="nb" style="color: #0086b3;">sort</span><span class="p">(</span><span class="nv" style="color: teal;">$a</span><span class="p">,</span><span class="nv" style="color: teal;">$b</span><span class="p">));</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$filehash</span><span class="p">{</span><span class="nv" style="color: teal;">$id</span><span class="p">}</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"> <span class="nv" style="color: teal;">$flag</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="s" style="color: #d14;">"Found duplicate: $a vs $b\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"> <span class="p">}</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$flag</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$_</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"> <span class="p">}</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"><span class="p">}</span></span></pre>
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