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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ssake">Debian Med / ssake</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c">83012ff7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-18T16:27:02+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.0</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#655bef3f57ab4f4cce2072bc957090f9f1136463">
SSAKE
</a>
</li>
<li class="file-stats">
<a href="#ce1391b705600df03b7d1bc02b64ed829bcf3848">
<span class="deleted-file">
−
SSAKE-readme.pdf
</span>
</a>
</li>
<li class="file-stats">
<a href="#275d783e298228506068436512433d343feb52aa">
SSAKE-readme.txt
→
readme.md
</a>
</li>
<li class="file-stats">
<a href="#99941e9e7cb4d8668499d7b495fec173b79dede0">
<span class="new-file">
+
test/CelegansLinkedReadsAssembly.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#c804969e079f8fb2205eca3e5403309119ac68c0">
test/Herpesvirus_3.60kb.reads.fa
</a>
</li>
<li class="file-stats">
<a href="#d6856a74a2823192c06c0ea5c349467fc7e5781e">
test/Herpesvirus_3.60kb.seed.fa
</a>
</li>
<li class="file-stats">
<a href="#ffca57aa66e6a0dffe01e71bc059138782a383a7">
test/HiSeqFusobacteriumAssembly.sh
</a>
</li>
<li class="file-stats">
<a href="#5a72107eda85078f1e628667ed138e70e45b15e2">
test/MiSeqCampylobacterAssembly.sh
</a>
</li>
<li class="file-stats">
<a href="#b03c5a3c850e023f0834b423398ebc5389d35400">
test/MiSeqCampylobacterAssemblyPIPELINE.sh
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</li>
<li class="file-stats">
<a href="#14067394c88a5c00f20cfec36a49e779ab061911">
test/MiSeqEbolaAssemblyPIPELINE.sh
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<li class="file-stats">
<a href="#a84f0d42402c7712ae52503a83988613be924e06">
test/MiSeqEcoliAssembly250XPE300.sh
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<li class="file-stats">
<a href="#d1969d87e396fe52d20be461548207ca94101d6e">
test/README.txt
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<li class="file-stats">
<a href="#bd0bfa40a3704cac54c450ad67c66e1937008247">
<span class="new-file">
+
test/assembly_metrics_tests.txt
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</li>
<li class="file-stats">
<a href="#4317d430515b77194d5fa1f46803bc66ee04c5ce">
<span class="new-file">
+
test/runSSAKE.sh
</span>
</a>
</li>
<li class="file-stats">
<a href="#3bff68cb7d46800ec7431313d77e423cea4c9be2">
test/runSSAKE.sh
→
tools/runSSAKE.sh
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="655bef3f57ab4f4cce2072bc957090f9f1136463">
<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#655bef3f57ab4f4cce2072bc957090f9f1136463"><strong>SSAKE</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">@@ -2,13 +2,14 @@</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="perl"></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="LC3" class="line" lang="perl"></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="LC4" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#AUTHOR</span></span>
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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Rene Warren (c) 2006-201<span class="idiff left right">7</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Rene Warren (c) 2006-201<span class="idiff left right">8</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<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="perl"><span class="c1" style="color: #998; font-style: italic;"># Short Sequence Assembly by K-mer search and 3' Extension (SSAKE)</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># rwarren at bcgsc.ca</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#NAME</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># SSAKE Rene Warren, April 2017</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" 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="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v3.8.5+ Implements targeted de novo assembly. Bug fix (only affected targeted de novo assembly -s mode)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="12" 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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># SSAKE Rene Warren, Jan 2018</span></span>
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<td class="diff-line-num new old_line" data-linenumber="12" 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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v4.0+ Initial support for linked reads (reads co-located to genomic locus via barcode or other means)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="12" 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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v3.8.5+ Bug fix (only affected targeted de novo assembly -s mode)</span></span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v3.8.4+ Improvements to the TASR modules, recruiting pairs when reads have a k-mer match</span></span>
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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v3.8.3+ Included option to ignore reads making up the consensus base extension (-y)</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># v3.8.3+ Included tie-breaker option (-q) when determining consensus from equal-coverage bases </span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(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="38" style="width: 35px; color: rgba(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">@@ -37,7 +38,7 @@</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># If you use SSAKE, the SSAKE code or ideas, please cite our work</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="c1" style="color: #998; font-style: italic;">#LICENSE</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># SSAKE Copyright (c) 2006-201<span class="idiff left right">7</span> Canada's Michael Smith Genome Science Centre. All rights reserved.</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># SSAKE Copyright (c) 2006-201<span class="idiff left right">8</span> Canada's Michael Smith Genome Science Centre. All rights reserved.</span></span>
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41
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="perl"></span>
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43
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># This program is free software; you can redistribute it and/or</span></span>
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44
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># modify it under the terms of the GNU General Public License</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,29 +56,32 @@</td>
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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;">use</span> <span class="nv" style="color: teal;">strict</span><span class="p">;</span></span>
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56
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: teal;">Std</span><span class="p">;</span></span>
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57
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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;">use</span> <span class="nn" style="color: #555;">Net::</span><span class="nv" style="color: teal;">SMTP</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;">use</span> <span class="nv" style="color: teal;">vars</span> <span class="sx" style="color: #d14;">qw($opt_f $opt_m $opt_o $opt_v $opt_r $opt_p $opt_d $opt_<span class="idiff left right">k</span> $opt_a $opt_z $opt_e $opt_g $opt_s $opt_t $opt_b $opt_c $opt_x $opt_n $opt_h $opt_i $opt_w $opt_j $opt_q $opt_y $opt_u)</span><span class="p">;</span></span>
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59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right">l</span></span></span>
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60
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="perl"><span class="nv" style="color: teal;">getopts</span><span class="p">(</span><span class="s" style="color: #d14;">'f:m:o:v:r:p:d:<span class="idiff left right">k</span>:a:z:e:g:s:t:b:c:x:n:h:u:w:j:q:y:i:'</span><span class="p">);</span></span>
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61
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$base_overlap</span><span class="p">,</span><span class="nv" style="color: teal;">$min_overlap</span><span class="p">,</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span><span class="nv" style="color: teal;">$MIN_READ_LENGTH</span><span class="p">,</span><span class="nv" style="color: teal;">$SEQ_SLIDE</span><span class="p">,</span><span class="nv" style="color: teal;">$min_base_ratio</span><span class="p">,</span><span class="nv" style="color: teal;">$paired</span><span class="p">,</span><span class="nv" style="color: teal;">$min_links</span><span class="p">,</span><span class="nv" style="color: teal;">$max_link_ratio</span><span class="p">,</span><span class="nv" style="color: teal;">$contig_size_cutoff</span><span class="p">,</span><span class="nv" style="color: teal;">$insert_stdev</span><span class="p">,</span><span class="nv" style="color: teal;">$unpaired_file</span><span class="p">,</span><span class="nv" style="color: teal;">$seed_file</span><span class="p">,</span><span class="nv" style="color: teal;">$max_trim</span><span class="p">,</span><span class="nv" style="color: teal;">$base_name</span><span class="p">,</span><span class="nv" style="color: teal;">$tracked</span><span class="p">,</span><span class="nv" style="color: teal;">$forcetrack</span><span class="p">,</span><span class="nv" style="color: teal;">$max_count_trim</span><span class="p">,</span><span class="nv" style="color: teal;">$min_tig_overlap</span><span class="p">,</span><span class="nv" style="color: teal;">$npad_gaps</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$min_depth_of_coverage</span><span class="p">,</span><span class="nv" style="color: teal;">$tie_breaker</span><span class="p">,</span><span class="nv" style="color: teal;">$ignore_read</span><span class="p">,</span><span class="nv" style="color: teal;">$independent</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">15</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">21</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mf" style="color: #099;">0.7</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;"><span class="idiff left">4</span></span><span class="p"><span class="idiff">,</span></span><span class="mf" style="color: #099;"><span class="idiff right">0.50</span></span><span class="p">,</span><span class="mi" style="color: #099;">100</span><span class="p">,</span><span class="mf" style="color: #099;">0.75</span><span class="p">,</span><span class="s" style="color: #d14;">"no-g"</span><span class="p">,</span><span class="s" style="color: #d14;">"no-targetSeed"</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">1</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="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">vars</span> <span class="sx" style="color: #d14;">qw($opt_f $opt_m $opt_o $opt_v $opt_r $opt_p $opt_d $opt_<span class="idiff left right">l</span> $opt_a $opt_z $opt_e $opt_g $opt_s $opt_t $opt_b $opt_c $opt_x $opt_n $opt_h $opt_i $opt_w $opt_j $opt_q $opt_y $opt_u)</span><span class="p">;</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#<span class="idiff left right">k unused letters</span></span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="perl"><span class="nv" style="color: teal;">getopts</span><span class="p">(</span><span class="s" style="color: #d14;">'f:m:o:v:r:p:d:<span class="idiff left right">l</span>:a:z:e:g:s:t:b:c:x:n:h:u:w:j:q:y:i:'</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$base_overlap</span><span class="p">,</span><span class="nv" style="color: teal;">$min_overlap</span><span class="p">,</span><span class="nv" style="color: teal;">$verbose</span><span class="p">,</span><span class="nv" style="color: teal;">$MIN_READ_LENGTH</span><span class="p">,</span><span class="nv" style="color: teal;">$SEQ_SLIDE</span><span class="p">,</span><span class="nv" style="color: teal;">$min_base_ratio</span><span class="p">,</span><span class="nv" style="color: teal;">$paired</span><span class="p">,</span><span class="nv" style="color: teal;">$min_links</span><span class="p">,</span><span class="nv" style="color: teal;">$max_link_ratio</span><span class="p">,</span><span class="nv" style="color: teal;">$contig_size_cutoff</span><span class="p">,</span><span class="nv" style="color: teal;">$insert_stdev</span><span class="p">,</span><span class="nv" style="color: teal;">$unpaired_file</span><span class="p">,</span><span class="nv" style="color: teal;">$seed_file</span><span class="p">,</span><span class="nv" style="color: teal;">$max_trim</span><span class="p">,</span><span class="nv" style="color: teal;">$base_name</span><span class="p">,</span><span class="nv" style="color: teal;">$tracked</span><span class="p">,</span><span class="nv" style="color: teal;">$forcetrack</span><span class="p">,</span><span class="nv" style="color: teal;">$max_count_trim</span><span class="p">,</span><span class="nv" style="color: teal;">$min_tig_overlap</span><span class="p">,</span><span class="nv" style="color: teal;">$npad_gaps</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$min_depth_of_coverage</span><span class="p">,</span><span class="nv" style="color: teal;">$tie_breaker</span><span class="p">,</span><span class="nv" style="color: teal;">$ignore_read</span><span class="p">,</span><span class="nv" style="color: teal;">$independent</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">15</span><span class="p">,</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">21</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">,</span><span class="mf" style="color: #099;">0.7</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;"><span class="idiff left">5</span></span><span class="p"><span class="idiff">,</span></span><span class="mf" style="color: #099;"><span class="idiff right">0.3</span></span><span class="p">,</span><span class="mi" style="color: #099;">100</span><span class="p">,</span><span class="mf" style="color: #099;">0.75</span><span class="p">,</span><span class="s" style="color: #d14;">"no-g"</span><span class="p">,</span><span class="s" style="color: #d14;">"no-targetSeed"</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">10</span><span class="p">,</span><span class="mi" style="color: #099;">20</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</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="LC63" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[v<span class="idiff left right">3.8.5</span>]"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"[v<span class="idiff left right">4.0</span>]"</span><span class="p">;</span></span>
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64
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$dev</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"rwarren\@bcgsc.ca"</span><span class="p">;</span></span>
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65
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$per</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="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$MAX</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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67
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$MAX_TOP</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1500</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># this is the very maximum anchoring edge sequence that will be searched (designed for use with -s to prevent long searches)</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;">my</span> <span class="nv" style="color: teal;">$TRACK_COUNT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$LR_MAXDIST_APART</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">60000</span><span class="p">;</span></span>
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69
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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;">my</span> <span class="nv" style="color: teal;">$illuminaLengthCutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">500</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">### means all sequence reads greater than this are not illumina sequences</span></span>
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<td class="diff-line-num new old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$LOW_COVERAGE_TIG_IN_A_ROW</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;">### SEE THIS MANY CONTIGS IN A ROW HAVING < -w COVERAGE TO TERMINATE</span></span>
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"></span>
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71
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#-------------------------------------------------</span></span>
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC76" 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;">$opt_f</span> <span class="o" style="font-weight: 600;">||</span> <span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: teal;">$opt_w</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"Usage: $0 $version\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"<span class="idiff left right">\n</span>Usage: $0 $version\n"</span><span class="p">;</span></span>
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75
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-f File containing all the [paired (-p 1)] reads (required)\n"</span><span class="p">;</span></span>
</pre>
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76
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\t With -p 1:\n"</span><span class="p">;</span></span>
</pre>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\t! Target insert size must be indicated at the end of the header line (e.g. :<span class="idiff left right">200 for a 200bp insert</span>)\n"</span><span class="p">;</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\t! Target insert size must be indicated at the end of the header line (e.g. :<span class="idiff left right">400 for a 400bp fragment/insert size</span>)\n"</span><span class="p">;</span></span>
</pre>
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78
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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\t! Paired reads must be separated by \":\"\n"</span><span class="p">;</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\t >template_name:200\n\t ACGACACTATGCATAAGCAGACGAGCAGCGACGCAGCACG:GCGCACGACGCAGCACAGCAGCAGACGAC\n"</span><span class="p">;</span></span>
</pre>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-w Minimum depth of coverage allowed for contigs (e.g. -w 1 = process all reads [v3.7 behavior], required)\n"</span><span class="p">;</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\t >header:400 (or >header_barcode:400)\n\t ACGACACTATGCATAAGCAGACGAGCAGCGACGCAGCACG:GCGCACGACGCAGCACAGCAGCAGACGAC\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-g Fasta file containing unpaired sequence reads (optional)\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-w Minimum depth of coverage allowed for contigs (e.g. -w 1 = process all reads [v3.7 behavior], required, recommended -w 5)\n"</span><span class="p">;</span></span>
</pre>
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81
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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">" *The assembly will stop when 50+ contigs with coverage < -w have been seen.*\n"</span><span class="p">;</span></span>
</pre>
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82
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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-s Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)\n"</span><span class="p">;</span></span>
</pre>
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83
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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\t-i Independent (de novo) assembly i.e Targets used to recruit reads for de novo assembly, not guide/seed reference-based assemblies (-i 1 = yes (default), 0 = no, optional)\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,13 +99,13 @@ if(! $opt_f || ! $opt_w){</td>
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95
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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;">print</span> <span class="s" style="color: #d14;">"-q Break tie when no consensus base at position, pick random base (-q 1 = yes, default = no, optional)\n"</span><span class="p">;</span> </span>
</pre>
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96
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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;">print</span> <span class="s" style="color: #d14;">"-p Paired-end reads used? (-p 1 = yes, default = no, optional)\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-v Runs in verbose mode (-v 1 = yes, default = no, optional)\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
98
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<td class="diff-line-num new_line old" data-linenumber="102" 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="LC98" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"============ <span class="idiff left right">O</span>ptions below only considered with -p 1 ============\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="99" 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="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"============ <span class="idiff left right">scaffolding o</span>ptions below only considered with -p 1 ============\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-e Error (%) allowed on mean distance e.g. -e 0.75 == distance +/- 75% (default -e $insert_stdev, optional)\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="100" 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">
100
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<td class="diff-line-num new_line old" data-linenumber="104" 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="LC100" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-<span class="idiff left right">k</span> Minimum number of links (read pairs) to compute scaffold (default -k $min_links, optional)\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="101" 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="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-<span class="idiff left right">l</span> Minimum number of links (read pairs) to compute scaffold (default -k $min_links, optional)\n"</span><span class="p">;</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-a Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a $max_link_ratio, optional)\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-x Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -x $min_tig_overlap, optional)\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"-n N-pad gaps (-n 1 = yes, default = no $npad_gaps, optional)\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"<span class="idiff left right">-g Fasta file containing unpaired sequence reads (optional)</span>\n"</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>print "-x Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -x $min_tig_overlap, optional)\n";</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>print "-n N-pad gaps (-n 1 = yes, default = no $npad_gaps, optional)\n";</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"<span class="idiff left right">\nError: Missing mandatory options -f and -w.\n</span>\n"</span><span class="p">;</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="perl"><span class="p">}</span></span>
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106
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_f</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">@@ -111,7 +115,7 @@ $min_base_ratio = $opt_r if($opt_r);</td>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="perl"><span class="nv" style="color: teal;">$max_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_t</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_t</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="perl"><span class="nv" style="color: teal;">$verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_v</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_v</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="perl"><span class="nv" style="color: teal;">$paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_p</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_p</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="perl"><span class="nv" style="color: teal;">$min_links</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_<span class="idiff left">k</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff right">$opt_k</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="perl"><span class="nv" style="color: teal;">$min_links</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_<span class="idiff left">l</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff right">$opt_l</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="perl"><span class="nv" style="color: teal;">$max_link_ratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_a</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_a</span><span class="p">);</span></span>
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116
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="perl"><span class="nv" style="color: teal;">$contig_size_cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_z</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_z</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="perl"><span class="nv" style="color: teal;">$insert_stdev</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_e</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_e</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -146,7 +150,7 @@ if($opt_s && ! -e $opt_s){### seed file specified, but does not exist</td>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="perl"> <span class="nv" style="color: teal;">$independent</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$opt_i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$independent</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;">$independent</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$independent</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">""</span><span class="p">){</span></span>
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148
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="perl"> <span class="nv" style="color: teal;">$independent</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="perl"> <span class="nv" style="color: teal;">$space_restriction</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;">###restrict the space to that of the target when doing targeted de novo assembly<span class="idiff left right">,</span> -i mode</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="perl"> <span class="nv" style="color: teal;">$space_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">###restrict the space to that of the target when doing targeted de novo assembly -i mode</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="perl"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -156,25 +160,26 @@ if ($base_name eq ""){</td>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="perl"> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$file</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".ssake_m"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$min_overlap</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_o"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$base_overlap</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_r"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$min_base_ratio</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_t"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$max_trim</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_w"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$min_depth_of_coverage</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_q"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$tie_breaker</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_y"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$ignore_read</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">){</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="perl"> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"_e"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$insert_stdev</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_<span class="idiff left">k"</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">$min_links</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"_a"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$max_link_ratio</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"_z"</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">$contig_size_cutoff</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"_x"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$min_tig_overlap</span></span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_g-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$display_unpaired_file</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="perl"> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"_e"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$insert_stdev</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_<span class="idiff left">l"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_links</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"_a"</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">$max_link_ratio</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"_z"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$contig_size_cutoff</span></span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_g-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$display_unpaired_file</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_s</span><span class="p">){</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="perl"> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"_s-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$display_seed_file</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_i<span class="idiff left right">-</span>"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$independent</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_j-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$targetwordlen</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_u-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$space_restriction</span><span class="p">;</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="perl"> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"_s-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$display_seed_file</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_i"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$independent</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_j-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$targetwordlen</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_u-"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$space_restriction</span><span class="p">;</span></span>
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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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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$pid_num</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getpgrp</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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166
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="perl"> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"_pid"</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$pid_num</span><span class="p">;</span></span>
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167
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="perl"><span class="p">}</span></span>
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="perl"></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"<span class="idiff left right">.contigs</span>"</span><span class="p">;</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$singlet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"<span class="idiff left right">.singlets</span>"</span><span class="p">;</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$short</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"<span class="idiff left right">.shor</span>t"</span><span class="p">;</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"<span class="idiff left right">_contigs.fa</span>"</span><span class="p">;</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$singlet</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"<span class="idiff left right">_singlets.fa</span>"</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$short</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"<span class="idiff left right">_short.tx</span>t"</span><span class="p">;</span></span>
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172
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$log</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".log"</span><span class="p">;</span></span>
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173
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$scaffold</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".scaffolds"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$mergedtigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".mergedcontigs"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$issues</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".pairing_issues"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span></span>
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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".pairing_distribution.csv"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$covfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".coverage.csv"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$tracked</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;">my</span> <span class="nv" style="color: teal;">$scaffold_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_scaffolds.fa"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$mergedtigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_mergedcontigs.fa"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">#deprecated Jan 2018</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$issues</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_pairing-issues.txt"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$distribution</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_pairing-distribution.csv"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">);</span></span>
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<td class="diff-line-num new old_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">
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$covfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"_coverage.csv"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$tracked</span><span class="p">);</span></span>
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178
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<td class="diff-line-num new_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$rdpositionfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".readposition"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$tracked</span><span class="p">);</span></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$pileupfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$base_name</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">".pileup"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">);</span></span>
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180
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -210,8 +215,10 @@ if($min_base_ratio <= 0.5 || $min_base_ratio > 1){</td>
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210
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"\nRunning: $0 $version\n-f $file\n-s $seed_file\n\t-i $independent\n\t-j $targetwordlen\n\t-u $space_restriction\n-h $ignorehead\n-w $min_depth_of_coverage\n-m $min_overlap\n-o $base_overlap\n-r $min_base_ratio\n-t $max_trim\n-q $tie_breaker\n-y $ignore_read\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
211
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<td class="diff-line-num new_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
216
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$tracked</span><span class="p">){</span><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"-c $tracked\nCoverage: $covfile\nRead position: $rdpositionfile\n"</span><span class="p">;</span><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"Pileup: $pileupfile\n"</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: teal;">$independent</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$space_restriction</span><span class="p">);}</span></span>
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<td class="diff-line-num old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
212
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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$forcetrack</span><span class="p">){</span><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"-z $contig_size_cutoff\n"</span><span class="p">;}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">){</span><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"-p $paired\n-e $insert_stdev\n-k $min_links\n-a $max_link_ratio\n-x $min_tig_overlap\nUnpaired reads (optional) -g $unpaired_file\nScaffolds: $scaffold\nMerged contigs: $mergedtigs\nPairing issues: $issues\nPairing distance distribution: $distribution\n"</span><span class="p">;}</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="perl"><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"\nContigs: $contig\nSinglets: $singlet\n\nExcluded reads: $short\nLog: $log\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">){</span><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"-p $paired\n-e $insert_stdev\n-l $min_links\n-a $max_link_ratio\nUnpaired reads (optional) -g $unpaired_file\nScaffold layout: $scaffold\nPairing issues: $issues\nPairing distance distribution: $distribution\n"</span><span class="p">;}</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="perl"><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"\nSinglets: $singlet\nContigs: $contig\n"</span><span class="p">;</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">){</span><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"Scaffolds: $scaffold_fasta\n"</span><span class="p">;}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="perl"><span class="nv" style="color: teal;">$init_message</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">"\nExcluded reads: $short\nLog: $log\n"</span><span class="p">;</span></span>
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215
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="perl"></span>
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216
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223
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$init_message</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="perl"><span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$init_message</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">@@ -238,23 +245,33 @@ if(-e $opt_s){</td>
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238
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$use_seed_message</span><span class="p">;</span></span>
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239
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$use_seed_message</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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240
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seed</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</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;">loadSeed</span><span class="p">(</span><span class="nv" style="color: teal;">$opt_s</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">);</span> </span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="perl"></span>
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span><span class="p">(</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$matepair</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
244
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="perl"><span class="p">(</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$matepair</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;">readFasta</span><span class="p">(</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$file</span><span class="p">,</span><span class="nv" style="color: teal;">$short</span><span class="p">,</span><span class="nv" style="color: teal;">$paired</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">);</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="perl"><span class="p">(</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$matepair</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;">readFasta</span><span class="p">(</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$unpaired_file</span><span class="p">,</span><span class="nv" style="color: teal;">$short</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">)</span> <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;">$opt_g</span><span class="p">);</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="perl"></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="perl"><span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span> <span class="nv" style="color: teal;">$opt_s</span><span class="p">){</span><span class="c1" style="color: #998; font-style: italic;">### not file provided as seed sequences</span></span>
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<td class="diff-line-num old old_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="perl"> <span class="nv" style="color: teal;">$seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$set</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">### the sequencing read set</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="perl"> <span class="nv" style="color: teal;">$TRACK_COUNT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> </span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="perl"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">### file provided as seed</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$independent</span><span class="p">){</span><span class="c1" style="color: #998; font-style: italic;">### de novo targeted assembly</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span><span class="p">(</span><span class="nv" style="color: teal;">$sumall</span><span class="p">,</span><span class="nv" style="color: teal;">$ctall</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">0</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="LC255" class="line" lang="perl"></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="perl"><span class="p">(</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$sumall</span><span class="p">,</span><span class="nv" style="color: teal;">$ctall</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">readFasta</span><span class="p">(</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$file</span><span class="p">,</span><span class="nv" style="color: teal;">$short</span><span class="p">,</span><span class="nv" style="color: teal;">$paired</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">,</span><span class="nv" style="color: teal;">$sumall</span><span class="p">,</span><span class="nv" style="color: teal;">$ctall</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="perl"><span class="p">(</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$sumall</span><span class="p">,</span><span class="nv" style="color: teal;">$ctall</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">readFasta</span><span class="p">(</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$unpaired_file</span><span class="p">,</span><span class="nv" style="color: teal;">$short</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">,</span><span class="nv" style="color: teal;">$sumall</span><span class="p">,</span><span class="nv" style="color: teal;">$ctall</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">e</span> <span class="nv" style="color: teal;">$opt_g</span><span class="p">);</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$sumall</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">3000000000</span><span class="p">;</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$statslog</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Total reads interrogated (total bases): $ctall ($sumall) -- human genome equivalent(s) = %.4f\n"</span><span class="p">;</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="perl"><span class="nb" style="color: #0086b3;">printf</span> <span class="nv" style="color: teal;">$statslog</span><span class="p">,</span> <span class="nv" style="color: teal;">$fc</span><span class="p">;</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="perl"><span class="nb" style="color: #0086b3;">printf</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$statslog</span><span class="p">,</span> <span class="nv" style="color: teal;">$fc</span><span class="p">;</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="perl"></span>
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264
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<pre style="margin: 0;">+<span id="LC264" 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;">$opt_s</span><span class="p">){</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="perl"> <span class="nv" style="color: teal;">$seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$set</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="perl"> <span class="nv" style="color: teal;">$TRACK_COUNT</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="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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="perl"><span class="p">}</span><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="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="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$independent</span><span class="p">){</span></span>
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252
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ind_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-i has been set to 1, which means the target sequences are USED for recruiting reads for de novo assembly, NOT target-based reference guided assemblies\n"</span><span class="p">;</span></span>
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253
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">printf</span> <span class="nv" style="color: teal;">$ind_message</span><span class="p">;</span></span>
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254
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<td class="diff-line-num new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$ind_message</span><span class="p">;</span></span>
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255
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="perl"> <span class="nv" style="color: teal;">$seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{};</span></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="perl"> <span class="nv" style="color: teal;">$seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$set</span><span class="p">;</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">### the sequencing read set</span></span></span>
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<td class="diff-line-num old old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
257
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<td class="diff-line-num new_line old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">### seed-guided assembly extension</span></span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="perl"> <span class="nv" style="color: teal;">$seed</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$set</span><span class="p">;</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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258
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ind_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-i has been set to 0, which means the target sequences are USED for recruiting reads for target-based reference guided assemblies (only de novo extension on the ends\n"</span><span class="p">;</span></span>
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259
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">printf</span> <span class="nv" style="color: teal;">$ind_message</span><span class="p">;</span></span>
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260
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$ind_message</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">@@ -300,11 +317,13 @@ print "$status_bar\n.";</td>
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300
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$keys_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="p">(</span> <span class="nv" style="color: teal;">%$seed</span> <span class="p">);</span></span>
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301
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$low_total</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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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$prev_cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#--------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="perl"><span class="nv" style="color: teal;">ASSEMBLY:</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seq</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">{</span><span class="nv" style="color: teal;">$seed</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$b</span><span class="p">}{</span><span class="s" style="color: #d14;">'count'</span><span class="p">}</span><span class="sr" style="color: #009926;"><=></span><span class="nv" style="color: teal;">$seed</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="p">}{</span><span class="s" style="color: #d14;">'count'</span><span class="p">}}</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%$seed</span><span class="p">){</span><span class="c1" style="color: #998; font-style: italic;">#cycle through the input [normalized] reads</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="perl"><span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seq</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%$seed</span><span class="p">){</span><span class="c1" style="color: #998; font-style: italic;">#cycle through the input [normalized] reads</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#foreach my $seq (sort {$seed->{$a}{'count'}<=>$seed->{$b}{'count'}} keys %$seed){#cycle through the input [normalized] reads</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#foreach my $seq (sort {$seed->{$b}{'count'}<=>$seed->{$a}{'count'}} keys %$seed){#cycle through the input [normalized] reads</span></span>
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308
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$track</span><span class="p">;</span></span>
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309
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328
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="perl"></span>
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310
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$pu_seed_name</span><span class="p">,</span><span class="nv" style="color: teal;">$pu_seed_ori</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span><span class="s" style="color: #d14;">""</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">@@ -335,25 +354,27 @@ foreach my $seq (sort {$seed->{$b}{'count'}<=>$seed->{$a}{'count'}} keys %$seed)</td>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$seed</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">deleteData</span><span class="p">(</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$seed</span><span class="p">,</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">#remove k-mer from hash table and prefix tree</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="perl"> </span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\n\n>>> START SEED SEQUENCE :: $seq <<<\n\n"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="perl"></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p"><span class="idiff left">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">doExtension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"3 prime"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$orig_mer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$set</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$bin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$reads_needed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$total_bases</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$base_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_base_ratio</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$verbose</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$track</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$forcetrack</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$tig_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$max_trim</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$encoded</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$matepair</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$tie_breaker</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$ignore_read</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$barcodeList</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$barcodeList</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">doExtension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"3 prime"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$orig_mer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$set</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$bin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$reads_needed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$total_bases</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$base_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_base_ratio</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$verbose</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$track</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$forcetrack</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$tig_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$max_trim</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$encoded</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$matepair</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$tie_breaker</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$ignore_read</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$barcodeList</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">####end of 3' extension, beginning of 5' extension (via 3' RC)</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seqrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">reverseComplement</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seqrc</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p"><span class="idiff left">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">doExtension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"5 prime"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$orig_mer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$seqrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$set</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$bin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$reads_needed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$total_bases</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$base_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_base_ratio</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$verbose</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$track</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$forcetrack</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$tig_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$max_trim</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$encoded</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$matepair</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$tie_breaker</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$ignore_read</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seqrc</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$barcodeList</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">doExtension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"5 prime"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$orig_mer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$seqrc</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$set</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$bin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$reads_needed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$total_bases</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$base_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_base_ratio</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$verbose</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$track</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$forcetrack</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$tig_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$max_trim</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$encoded</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$matepair</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$tie_breaker</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$ignore_read</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$barcodeList</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">####end of 5' extension</span></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$leng</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seqrc</span><span class="p">);</span></span>
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345
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$reversetig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">reverseComplement</span><span class="p">(</span><span class="nv" style="color: teal;">$seqrc</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">### return to sequence, as provided </span></span>
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346
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365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$trimmed_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$start_sequence</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="nv" style="color: teal;">$max_trim</span><span class="p">);</span></span>
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347
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="perl"></span>
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348
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$leng</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$trimmed_length</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nv" style="color: teal;">$reads_needed</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$opt_s</span><span class="p">)){</span> <span class="c1" style="color: #998; font-style: italic;">### second conditional is similar to TASR, output contig if targeted assembly mode and more reads have been recruited.</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span> <span class="nv" style="color: teal;">ASSEMBLY</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$low_total</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$LOW_COVERAGE_TIG_IN_A_ROW</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">### sudden termination based on expected depth ov coverage</span></span>
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349
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### commented out: && $start_sequence ne $seqrc && $start_sequence ne $reversetig</span></span>
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350
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="perl"> <span class="nv" style="color: teal;">$tig_length</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$tig_count</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$leng</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="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$total_bases</span> <span class="o" style="font-weight: 600;">/</span> <span class="nv" style="color: teal;">$leng</span><span class="p">;</span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="perl"> <span class="nv" style="color: teal;">$low_total</span><span class="o" style="font-weight: 600;">++</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$cov</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$min_depth_of_coverage</span><span class="p">);</span></span>
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353
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="perl"> <span class="k" style="font-weight: 600;">last</span> <span class="nv" style="color: teal;">ASSEMBLY</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$low_total</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">50</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">### sudden termination based on expected depth ov coverage</span></span>
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354
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$total_bases</span> <span class="o" style="font-weight: 600;">/</span> <span class="nv" style="color: teal;">$leng</span><span class="p">;</span></span>
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355
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">printf</span> <span class="nv" style="color: teal;">TIG</span> <span class="s" style="color: #d14;">">contig%i|size%i|read%i|cov%.2f$seed_name\n%s\n"</span><span class="p">,</span> <span class="p">(</span><span class="nv" style="color: teal;">$tig_count</span><span class="p">,</span><span class="nv" style="color: teal;">$leng</span><span class="p">,</span><span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span><span class="nv" style="color: teal;">$cov</span><span class="p">,</span><span class="nv" style="color: teal;">$reversetig</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">#print contigs to file</span></span>
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356
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="perl"> <span class="nv" style="color: teal;">$tig_length</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$tig_count</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$leng</span><span class="p">;</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#if($prev_cov >= $min_depth_of_coverage){ $low_total=0; }###JAN2018 NEED $LOW_COVERAGE_TIG_IN_A_ROW to TERMINATE</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="perl"> <span class="nv" style="color: teal;">$low_total</span><span class="o" style="font-weight: 600;">++</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$cov</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$min_depth_of_coverage</span><span class="p">);</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="perl"></span>
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357
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$forcetrack</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$leng</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$contig_size_cutoff</span><span class="p">){</span></span>
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358
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="perl"></span>
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359
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$tracked</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">### only execute & report if user specifies -c</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="477" style="width: 35px; color: rgba(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="498" style="width: 35px; color: rgba(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">@@ -477,7 +498,7 @@ foreach my $seq (sort {$seed->{$b}{'count'}<=>$seed->{$a}{'count'}} keys %$seed)</td>
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477
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="perl"> <span class="p">}</span></span>
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478
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499
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$track_all</span><span class="p">,</span><span class="nv" style="color: teal;">$alternate</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;">trackReads</span><span class="p">(</span><span class="nv" style="color: teal;">$track</span><span class="p">,</span><span class="nv" style="color: teal;">$track_all</span><span class="p">,</span><span class="nv" style="color: teal;">$alternate</span><span class="p">,</span><span class="nv" style="color: teal;">$tig_count</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">### all pairs from all contigs (track for scaffolding)</span></span>
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479
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="perl"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="perl"> <span class="nv" style="color: teal;">$prev_cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$cov</span><span class="p">;</span></span>
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481
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502
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="perl"> <span class="nv" style="color: teal;">$tig_count</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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482
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503
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<pre style="margin: 0;"> <span id="LC503" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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504
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<pre style="margin: 0;"> <span id="LC504" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cov</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -551,20 +572,40 @@ if($paired){</td>
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551
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$sc_end_message</span><span class="p">;</span></span>
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552
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573
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="perl"> <span class="nv" style="color: teal;">$assemblyruninfo</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$sc_end_message</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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553
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574
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="perl"></span>
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554
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$me_start_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"\n=>Merging contigs initiated $date\n"</span><span class="p">;</span></span>
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555
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$me_start_message</span><span class="p">;</span></span>
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556
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<pre style="margin: 0;">-<span id="LC556" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$me_start_message</span><span class="p">;</span></span>
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557
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<pre style="margin: 0;">-<span id="LC557" class="line" lang="perl"> <span class="nv" style="color: teal;">$assemblyruninfo</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$me_start_message</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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558
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<pre style="margin: 0;">-<span id="LC558" class="line" lang="perl"></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="perl"></span>
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560
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">forcefillGaps</span><span class="p">(</span><span class="nv" style="color: teal;">$scaffold</span><span class="p">,</span> <span class="nv" style="color: teal;">$contig</span><span class="p">,</span> <span class="nv" style="color: teal;">$mergedtigs</span><span class="p">,</span> <span class="nv" style="color: teal;">$verbose</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_tig_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$max_count_trim</span><span class="p">,</span> <span class="nv" style="color: teal;">$npad_gaps</span><span class="p">,</span> <span class="nv" style="color: teal;">$alternate</span><span class="p">,</span> <span class="nv" style="color: teal;">$matepair</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$base_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_base_ratio</span><span class="p">,</span> <span class="nv" style="color: teal;">$forcetrack</span><span class="p">,</span> <span class="nv" style="color: teal;">$max_trim</span><span class="p">,</span> <span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$insert_stdev</span><span class="p">);</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="perl"></span>
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562
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575
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="perl"> <span class="nv" style="color: teal;">$date</span> <span class="o" style="font-weight: 600;">=</span> <span class="sb" style="color: #d14;">`date`</span><span class="p">;</span></span>
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563
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576
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">(</span><span class="nv" style="color: teal;">$date</span><span class="p">);</span></span>
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564
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$me_end_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"\nMerging contigs ended $date\n"</span><span class="p">;</span></span>
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565
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$me_end_message</span><span class="p">;</span></span>
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566
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<pre style="margin: 0;">-<span id="LC566" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$me_end_message</span><span class="p">;</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="perl"> <span class="nv" style="color: teal;">$assemblyruninfo</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$me_end_message</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="perl"></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$sc_fasta_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"\n\n=>Making scaffold FASTA file: $date\n"</span><span class="p">;</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$sc_fasta_message</span><span class="p">;</span></span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$sc_fasta_message</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="perl"> <span class="nv" style="color: teal;">$assemblyruninfo</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$sc_fasta_message</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### reading contigs to make fasta file and get additional needed info</span></span>
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<td class="diff-line-num new new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$tighash</span><span class="p">,</span> <span class="nv" style="color: teal;">$tignames</span><span class="p">,</span> <span class="nv" style="color: teal;">$tig_length</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;">readContigsMemory</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">);</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### building scaffold fasta </span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="perl"> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">buildScaffoldFasta</span><span class="p">(</span><span class="nv" style="color: teal;">$scaffold</span><span class="p">,</span><span class="nv" style="color: teal;">$tighash</span><span class="p">,</span><span class="nv" style="color: teal;">$scaffold_fasta</span><span class="p">);</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="perl"></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$sc_fasta_done_message</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Scaffolds FASTA in: $scaffold_fasta\n"</span><span class="p">;</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">$sc_fasta_done_message</span><span class="p">;</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$sc_fasta_done_message</span><span class="p">;</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="perl"> <span class="nv" style="color: teal;">$assemblyruninfo</span><span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$sc_fasta_done_message</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="perl"></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### DEPRECATED FEATURE JAN2018 (force-fill gap)</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#$date = `date`;</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#chomp($date);</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#my $me_start_message = "\n=>Merging contigs initiated $date\n";</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print $me_start_message;</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print LOG $me_start_message;</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#$assemblyruninfo.= $me_start_message . "\n";</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="perl"></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#&forcefillGaps($scaffold, $contig, $mergedtigs, $verbose, $min_tig_overlap, $max_count_trim, $npad_gaps, $alternate, $matepair, $min_overlap, $base_overlap, $min_base_ratio, $forcetrack, $max_trim, $encoded,$seedsplit,$space_restriction,$targetwordlen,$insert_stdev);</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="perl"></span>
</pre>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#$date = `date`;</span></span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#chomp($date);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="605" 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">
605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#my $me_end_message = "\nMerging contigs ended $date\n";</span></span>
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<td class="diff-line-num new new_line" data-linenumber="606" 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">
606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print $me_end_message;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="607" 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">
607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print LOG $me_end_message;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#$assemblyruninfo.= $me_end_message . "\n";</span></span>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="perl"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="perl"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1010,7 +1051,7 @@ sub pairContigs{</td>
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1010
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1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># SSAKE contig extension</span></span>
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1011
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1052
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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">doExtension</span><span class="p">{</span></span>
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1012
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1053
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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="perl"></span>
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1013
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<pre style="margin: 0;">-<span id="LC1013" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$direction</span><span class="p">,</span> <span class="nv" style="color: teal;">$orig_mer</span><span class="p">,</span> <span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$base_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_base_ratio</span><span class="p">,</span> <span class="nv" style="color: teal;">$verbose</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p">,</span> <span class="nv" style="color: teal;">$paired</span><span class="p">,</span> <span class="nv" style="color: teal;">$tig_count</span><span class="p">,</span> <span class="nv" style="color: teal;">$max_trim</span><span class="p">,</span> <span class="nv" style="color: teal;">$e</span><span class="p">,</span> <span class="nv" style="color: teal;">$matepair</span><span class="p">,</span> <span class="nv" style="color: teal;">$tie_breaker</span><span class="p">,</span> <span class="nv" style="color: teal;">$ignore_read</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>
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1054
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<pre style="margin: 0;">+<span id="LC1054" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$direction</span><span class="p">,</span> <span class="nv" style="color: teal;">$orig_mer</span><span class="p">,</span> <span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$base_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_base_ratio</span><span class="p">,</span> <span class="nv" style="color: teal;">$verbose</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p">,</span> <span class="nv" style="color: teal;">$paired</span><span class="p">,</span> <span class="nv" style="color: teal;">$tig_count</span><span class="p">,</span> <span class="nv" style="color: teal;">$max_trim</span><span class="p">,</span> <span class="nv" style="color: teal;">$e</span><span class="p">,</span> <span class="nv" style="color: teal;">$matepair</span><span class="p">,</span> <span class="nv" style="color: teal;">$tie_breaker</span><span class="p">,</span> <span class="nv" style="color: teal;">$ignore_read</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$barcodeList</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>
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1014
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1055
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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="perl"></span>
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1015
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1056
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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$extended</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1016
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1057
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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$trim_ct</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;">#trim counter - keeps track of 3'-end trim</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1023" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1023,7 +1064,43 @@ sub doExtension{</td>
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1023
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1064
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<pre style="margin: 0;"> <span id="LC1064" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$growing_tig_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">);</span></span>
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1024
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1065
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<pre style="margin: 0;"> <span id="LC1065" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$pos</span><span class="p">,</span><span class="nv" style="color: teal;">$span</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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1025
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1066
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<pre style="margin: 0;"> <span id="LC1066" class="line" lang="perl"></span>
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1067
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<pre style="margin: 0;">+<span id="LC1067" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### Added 15January18 =====================================</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1068" 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">
1068
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<pre style="margin: 0;">+<span id="LC1068" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$growing_tig_length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$MAX</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># $seq is length of contig being extended -- if larger than largest read, make sure the largest read could align and all subsequent rds.</span></span>
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1069
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<pre style="margin: 0;">+<span id="LC1069" class="line" lang="perl"> <span class="nv" style="color: teal;">$span</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$MAX</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$TRACK_COUNT</span><span class="p">;</span></span>
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1070
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<pre style="margin: 0;">+<span id="LC1070" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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1071
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<pre style="margin: 0;">+<span id="LC1071" class="line" lang="perl"> <span class="nv" style="color: teal;">$span</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$growing_tig_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$TRACK_COUNT</span><span class="p">;</span></span>
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1072
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<pre style="margin: 0;">+<span id="LC1072" class="line" lang="perl"> <span class="p">}</span></span>
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1073
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<pre style="margin: 0;">+<span id="LC1073" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="1074" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1074
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<pre style="margin: 0;">+<span id="LC1074" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### NEW ADD JAN 2018</span></span>
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1075
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<pre style="margin: 0;">+<span id="LC1075" class="line" lang="perl"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="nv" style="color: teal;">$span</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$min_overlap</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># will slide the subseq, until the user-defined min overlap size</span></span>
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1076
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<pre style="margin: 0;">+<span id="LC1076" class="line" lang="perl"> <span class="nv" style="color: teal;">$pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$growing_tig_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$span</span><span class="p">;</span></span>
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1077
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<pre style="margin: 0;">+<span id="LC1077" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"MAX:$MAX, SPAN:$span, POS:$pos"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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1078
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<pre style="margin: 0;">+<span id="LC1078" class="line" lang="perl"></span>
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1079
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<pre style="margin: 0;">+<span id="LC1079" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$subseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$pos</span><span class="p">,</span> <span class="nv" style="color: teal;">$span</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">#make a sub-sequence of length l-(1..i) for searching</span></span>
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1080
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<pre style="margin: 0;">+<span id="LC1080" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$subseq</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\S{4}/g</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1081
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<pre style="margin: 0;">+<span id="LC1081" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$subset</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$bin</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$s</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$s</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$s</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$s</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]}};</span> <span class="c1" style="color: #998; font-style: italic;">#Will grab everything even the reverse complement ones</span></span>
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1082
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<pre style="margin: 0;">+<span id="LC1082" class="line" lang="perl"></span>
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1083
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<pre style="margin: 0;">+<span id="LC1083" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"####$direction SEARCH Position:$pos Span:$span - Subseq:$subseq Previous:$seq\n"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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1084
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<pre style="margin: 0;">+<span id="LC1084" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="1085" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1085
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<pre style="margin: 0;">+<span id="LC1085" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### SEARCH -- this cycles through limited k-mer space</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1086
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<pre style="margin: 0;">+<span id="LC1086" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$pass</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$b</span><span class="p">}</span> <span class="sr" style="color: #009926;"><=></span> <span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="p">}}</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%$subset</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1087
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<pre style="margin: 0;">+<span id="LC1087" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$pass</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^$subseq([ACGT]+)/</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$subseq</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/$pass/</span><span class="p">){</span><span class="c1" style="color: #998; font-style: italic;">#### OVERHANG || EMBEDDED</span></span>
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1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print "BC $subset->{$pass}\n";</span></span>
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1089
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<pre style="margin: 0;">+<span id="LC1089" 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="nv" style="color: teal;">$barcodeList</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$pass</span><span class="p">}}){</span><span class="c1" style="color: #998; font-style: italic;">### barcode seen before</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1090
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<pre style="margin: 0;">+<span id="LC1090" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$barcodeList</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$pass</span><span class="p">}}{</span><span class="s" style="color: #d14;">'lastlength'</span><span class="p">})</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$LR_MAXDIST_APART</span><span class="p">){</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1026" 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="1091" 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">
1091
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<pre style="margin: 0;">+<span id="LC1091" class="line" lang="perl"> <span class="nv" style="color: teal;">$barcodeList</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$pass</span><span class="p">}}{</span><span class="s" style="color: #d14;">'count'</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="c1" style="color: #998; font-style: italic;">### reset barcode to zero, too far apart, new molecule</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1092" 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">
1092
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<pre style="margin: 0;">+<span id="LC1092" class="line" lang="perl"> <span class="p">}</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="1093" 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">
1093
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<pre style="margin: 0;">+<span id="LC1093" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1026" 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="1094" 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">
1094
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<pre style="margin: 0;">+<span id="LC1094" class="line" lang="perl"> <span class="nv" style="color: teal;">$barcodeList</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$pass</span><span class="p">}}{</span><span class="s" style="color: #d14;">'lastlength'</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">### new tracks all barcodes encountered</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1095
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<pre style="margin: 0;">+<span id="LC1095" class="line" lang="perl"> <span class="nv" style="color: teal;">$barcodeList</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$pass</span><span class="p">}}{</span><span class="s" style="color: #d14;">'count'</span><span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">### new tracks all barcodes encountered</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1096" 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">
1096
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<pre style="margin: 0;">+<span id="LC1096" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1097" 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">
1097
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<pre style="margin: 0;">+<span id="LC1097" class="line" lang="perl"> <span class="p">}</span> </span>
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1098
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<pre style="margin: 0;">+<span id="LC1098" class="line" lang="perl"> <span class="nv" style="color: teal;">$span</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="1099" 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">
1099
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<pre style="margin: 0;">+<span id="LC1099" class="line" lang="perl"> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">#while overlap >= user-defined -m minimum</span></span>
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1100
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<pre style="margin: 0;">+<span id="LC1100" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="1101" 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">
1101
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<pre style="margin: 0;">+<span id="LC1101" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### END NEW ADDITION==========================================</span></span>
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1026
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<td class="diff-line-num new_line" data-linenumber="1102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1102
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<pre style="margin: 0;"> <span id="LC1102" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### Added 19March08</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1027" 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="1103" 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">
1103
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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$pos</span><span class="p">,</span><span class="nv" style="color: teal;">$span</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1027
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<td class="diff-line-num new_line" data-linenumber="1104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1104
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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$growing_tig_length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$MAX</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;"># $seq is length of contig being extended -- if larger than largest read, make sure the largest read could align and all subsequent rds.</span></span>
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<td class="diff-line-num old_line" data-linenumber="1028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1028
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<td class="diff-line-num new_line" data-linenumber="1105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1105
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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="perl"> <span class="nv" style="color: teal;">$span</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$MAX</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$TRACK_COUNT</span><span class="p">;</span></span>
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1029
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1106
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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1052" style="width: 35px; color: rgba(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="1129" style="width: 35px; color: rgba(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">@@ -1052,7 +1129,6 @@ sub doExtension{</td>
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1052
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1129
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<pre style="margin: 0;"> <span id="LC1129" class="line" lang="perl"></span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="1130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1130
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<pre style="margin: 0;"> <span id="LC1130" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">### SEARCH -- this cycles through limited k-mer space</span></span>
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1054
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1131
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<pre style="margin: 0;"> <span id="LC1131" 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;">$pass</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">sort</span> <span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$b</span><span class="p">}</span> <span class="sr" style="color: #009926;"><=></span> <span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$a</span><span class="p">}}</span> <span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%$subset</span><span class="p">){</span></span>
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1055
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<td class="diff-line-num new_line old" data-linenumber="1132" 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="LC1055" class="line" lang="perl"></span>
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1056
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1132
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<pre style="margin: 0;"> <span id="LC1132" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$pass</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^$subseq([ACGT]+)/</span><span class="p">){</span><span class="c1" style="color: #998; font-style: italic;">#### OVERHANG </span></span>
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1057
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<td class="diff-line-num new_line" data-linenumber="1133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1133
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#can we align perfectly that subseq to another rd start?</span></span>
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1058
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1134
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$dangle</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 unfold js-unfold old_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="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1074,8 +1150,7 @@ sub doExtension{</td>
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1074
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1150
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<pre style="margin: 0;"> <span id="LC1150" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">###############################################</span></span>
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1075
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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="c1" style="color: #998; font-style: italic;"># CONSIDER CERTAIN READS FOR OVERLAP, PREFERABLY THOSE WITH LOGICAL MATES AND FWD READS IN TIG LARGE ENOUGH TO HAVE SUCH PAIRS</span></span>
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1076
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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;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$newpass</span><span class="p">(</span><span class="nb" style="color: #0086b3;">keys</span> <span class="nv" style="color: teal;">%$psr</span><span class="p">){</span></span>
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1077
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<pre style="margin: 0;">-<span id="LC1077" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$paired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$matepair</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: teal;">$psr</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'end'</span><span class="p">}</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$psr</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'start'</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: teal;">$psr</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'start'</span><span class="p">}</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$set</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'grace'</span><span class="p">})){</span><span class="c1" style="color: #998; font-style: italic;">#paired, pairingRds, <---, outside grace</span></span>
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1078
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<pre style="margin: 0;">-<span id="LC1078" class="line" lang="perl"></span>
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1153
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<pre style="margin: 0;">+<span id="LC1153" 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;">$seq</span><span class="p">)</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">2000</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">((</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">2000</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">)</span><span class="o" style="font-weight: 600;"><=</span><span class="mi" style="color: #099;">10000</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$barcodeList</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}}{</span><span class="s" style="color: #d14;">'count'</span><span class="p">}</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">)</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">10000</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$barcodeList</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$subset</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}}{</span><span class="s" style="color: #d14;">'count'</span><span class="p">}</span><span class="o" style="font-weight: 600;">>=</span><span class="mi" style="color: #099;">9</span> <span class="p">)</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$paired</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">defined</span> <span class="nv" style="color: teal;">$matepair</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: teal;">$psr</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'end'</span><span class="p">}</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$psr</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'start'</span><span class="p">})</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="nv" style="color: teal;">$psr</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'start'</span><span class="p">}</span> <span class="o" style="font-weight: 600;">>=</span> <span class="nv" style="color: teal;">$set</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$newpass</span><span class="p">}{</span><span class="s" style="color: #d14;">'grace'</span><span class="p">})){</span><span class="c1" style="color: #998; font-style: italic;">#paired, pairingRds, <---, outside grace</span></span>
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1079
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1154
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<pre style="margin: 0;"> <span id="LC1154" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print "$B_end <-- $B_start *** [upper limit is grace]***\n";</span></span>
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1080
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1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># <--B</span></span>
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1081
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1156
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<pre style="margin: 0;"> <span id="LC1156" 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="1100" style="width: 35px; color: rgba(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="1175" style="width: 35px; color: rgba(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">@@ -1100,7 +1175,7 @@ sub doExtension{</td>
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1100
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1175
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<pre style="margin: 0;"> <span id="LC1175" class="line" lang="perl"> <span class="p">}</span></span>
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1101
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1176
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<pre style="margin: 0;"> <span id="LC1176" class="line" lang="perl"> <span class="p">}</span></span>
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1102
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1177
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<pre style="margin: 0;"> <span id="LC1177" class="line" lang="perl"> <span class="p">}</span></span>
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1103
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<pre style="margin: 0;">-<span id="LC1103" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">els<span class="idiff left right">e</span></span><span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">### not paired or paired (B-->): collect all overlaps</span></span>
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1178
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<pre style="margin: 0;">+<span id="LC1178" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">els<span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="mi" style="color: #099;"><span class="idiff">2000</span></span><span class="idiff"> </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="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff">2000</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><=</span></span><span class="mi" style="color: #099;"><span class="idiff">10000</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">$barcodeList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$subset</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$newpass</span></span><span class="p"><span class="idiff">}}{</span></span><span class="s" style="color: #d14;"><span class="idiff">'count'</span></span><span class="p"><span class="idiff">}</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">length</span></span><span class="p"><span class="idiff">(</span></span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="mi" style="color: #099;"><span class="idiff">10000</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">$barcodeList</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$subset</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="p"><span class="idiff">{</span></span><span class="nv" style="color: teal;"><span class="idiff">$newpass</span></span><span class="p"><span class="idiff">}}{</span></span><span class="s" style="color: #d14;"><span class="idiff">'count'</span></span><span class="p"><span class="idiff">}</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>=</span></span><span class="mi" style="color: #099;"><span class="idiff">9</span></span><span class="idiff"> </span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">)</span>{</span><span class="c1" style="color: #998; font-style: italic;">### not paired or paired (B-->): collect all overlaps</span></span>
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1104
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1179
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<pre style="margin: 0;"> <span id="LC1179" class="line" lang="perl"> <span class="nv" style="color: teal;">$overhang</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">collectOverhang</span><span class="p">(</span><span class="nv" style="color: teal;">$overhang</span><span class="p">,</span><span class="nv" style="color: teal;">$newpass</span><span class="p">,</span><span class="nv" style="color: teal;">$dangle</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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1105
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1180
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<pre style="margin: 0;"> <span id="LC1180" class="line" lang="perl"> <span class="nv" style="color: teal;">$overlapping_reads</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$pass</span><span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1106
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1181
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<pre style="margin: 0;"> <span id="LC1181" class="line" lang="perl"> <span class="nv" style="color: teal;">$long</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span> <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;">$newpass</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$illuminaLengthCutoff</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1108" style="width: 35px; color: rgba(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="1183" style="width: 35px; color: rgba(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">@@ -1108,7 +1183,6 @@ sub doExtension{</td>
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1108
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1183
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<pre style="margin: 0;"> <span id="LC1183" class="line" lang="perl"> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">###for $newpass</span></span>
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1109
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<td class="diff-line-num new_line" data-linenumber="1184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#----------------------------------</span></span>
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<td class="diff-line-num old_line" data-linenumber="1110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1110
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<td class="diff-line-num new_line" data-linenumber="1185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: teal;">$subseq</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/$pass/</span><span class="p">){</span> <span class="c1" style="color: #998; font-style: italic;">#### EMBEDDED</span></span>
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1111
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<pre style="margin: 0;">-<span id="LC1111" class="line" lang="perl"></span>
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1112
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1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$complement_pass</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">reverseComplement</span><span class="p">(</span><span class="nv" style="color: teal;">$pass</span><span class="p">);</span></span>
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1113
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1187
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<pre style="margin: 0;"> <span id="LC1187" class="line" lang="perl"></span>
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1114
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1188
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"$pass found in $subseq ($set->{$pass}{'count'}) - deleting read: $pass and complement ($set->{$complement_pass}): $complement_pass\n\n"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1133" style="width: 35px; color: rgba(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="1207" style="width: 35px; color: rgba(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">@@ -1133,7 +1207,7 @@ sub doExtension{</td>
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1133
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1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$current_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$complement_pass</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="nv" style="color: teal;">$current_reads</span><span class="p">;</span></span>
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1134
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1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="perl"> <span class="nv" style="color: teal;">$reads_needed</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$current_reads</span><span class="p">;</span></span>
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1135
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<td class="diff-line-num new_line" data-linenumber="1209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1209
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<pre style="margin: 0;"> <span id="LC1209" class="line" lang="perl"> <span class="nv" style="color: teal;">$total_bases</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$current_bases</span><span class="p">;</span></span>
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1136
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<pre style="margin: 0;">-<span id="LC1136" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">){</span><span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="1137" 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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1210
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<pre style="margin: 0;">+<span id="LC1210" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$paired</span><span class="p">){</span></span>
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1137
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<td class="diff-line-num new_line" data-linenumber="1211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1211
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<pre style="margin: 0;"> <span id="LC1211" class="line" lang="perl"> <span class="nv" style="color: teal;">$track</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$complement_pass</span><span class="p">}{</span><span class="s" style="color: #d14;">'end'</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$pos</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="1138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1138
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1212
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<pre style="margin: 0;"> <span id="LC1212" class="line" lang="perl"> <span class="nv" style="color: teal;">$track</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$complement_pass</span><span class="p">}{</span><span class="s" style="color: #d14;">'start'</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$pos</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$complement_pass</span><span class="p">);</span></span>
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1139
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1213
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<pre style="margin: 0;"> <span id="LC1213" class="line" lang="perl"> <span class="nv" style="color: teal;">$track</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$complement_pass</span><span class="p">}{</span><span class="s" style="color: #d14;">'cov'</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$current_reads</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1316" style="width: 35px; color: rgba(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="1390" style="width: 35px; color: rgba(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">@@ -1316,7 +1390,7 @@ sub doExtension{</td>
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1316
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1390
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<pre style="margin: 0;"> <span id="LC1390" class="line" lang="perl"> </span>
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<td class="diff-line-num old_line" data-linenumber="1317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1317
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1391
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<pre style="margin: 0;"> <span id="LC1391" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"\n*** NOTHING ELSE TO BE DONE IN $direction - PERHAPS YOU COULD DECREASE THE MINIMUM OVERLAP -m (currently set to -m $min_overlap) ***\n\n"</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$verbose</span><span class="p">);</span></span>
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1318
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1392
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<pre style="margin: 0;"> <span id="LC1392" class="line" lang="perl"></span>
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<td class="diff-line-num old old_line" data-linenumber="1319" 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">
1319
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<pre style="margin: 0;">-<span id="LC1319" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p">;</span></span>
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1393
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<pre style="margin: 0;">+<span id="LC1393" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span> <span class="nv" style="color: teal;">$bin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff right">$barcodeList</span></span><span class="p">;</span></span>
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1320
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1394
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1321
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1395
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<pre style="margin: 0;"> <span id="LC1395" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1322
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1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1347" style="width: 35px; color: rgba(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="1421" style="width: 35px; color: rgba(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">@@ -1347,7 +1421,7 @@ sub reverseComplement{</td>
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1347
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1421
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<pre style="margin: 0;"> <span id="LC1421" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1348
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1422
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<pre style="margin: 0;"> <span id="LC1422" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#-----------------</span></span>
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1349
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1423
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<pre style="margin: 0;"> <span id="LC1423" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">readFasta</span><span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1350" 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">
1350
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<td class="diff-line-num new_line old" data-linenumber="1424" 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="LC1350" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$file</span><span class="p">,</span><span class="nv" style="color: teal;">$short</span><span class="p">,</span><span class="nv" style="color: teal;">$paired</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>
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1424
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<pre style="margin: 0;">+<span id="LC1424" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$file</span><span class="p">,</span><span class="nv" style="color: teal;">$short</span><span class="p">,</span><span class="nv" style="color: teal;">$paired</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p"><span class="idiff left">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$sumall</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$ctall</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>
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1351
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<td class="diff-line-num new_line" data-linenumber="1425" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1425
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<pre style="margin: 0;"> <span id="LC1425" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1352" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1352
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<td class="diff-line-num new_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1426
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<pre style="margin: 0;"> <span id="LC1426" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ctrd</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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1353
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<td class="diff-line-num new_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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<pre style="margin: 0;"> <span id="LC1427" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ctline</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1372,6 +1446,10 @@ sub readFasta{</td>
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1372
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1446
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<pre style="margin: 0;"> <span id="LC1446" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$rd1</span><span class="p">,</span><span class="nv" style="color: teal;">$rd2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nv" style="color: teal;">$1</span><span class="p">,</span><span class="nv" style="color: teal;">$2</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1373
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<td class="diff-line-num new_line" data-linenumber="1447" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$head1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$head</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"1"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1374
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<td class="diff-line-num new_line" data-linenumber="1448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1448
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$head2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$head</span> <span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">"2"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">####num</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1450" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1450
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<pre style="margin: 0;">+<span id="LC1450" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$rd1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$rd2</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1451" 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">
1451
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<pre style="margin: 0;">+<span id="LC1451" class="line" lang="perl"> <span class="nv" style="color: teal;">$sumall</span><span class="o" style="font-weight: 600;">+=</span><span class="nv" style="color: teal;">$len</span><span class="p">;</span></span>
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1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="perl"> <span class="nv" style="color: teal;">$ctall</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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1375
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1453
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<pre style="margin: 0;"> <span id="LC1453" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1376
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<td class="diff-line-num new_line" data-linenumber="1454" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1454
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<pre style="margin: 0;"> <span id="LC1454" class="line" lang="perl"> <span class="nv" style="color: teal;">$head1</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1377
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<td class="diff-line-num new_line" data-linenumber="1455" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1455
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<pre style="margin: 0;"> <span id="LC1455" class="line" lang="perl"> <span class="nv" style="color: teal;">$head2</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1395,6 +1473,10 @@ sub readFasta{</td>
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1395
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1473
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<pre style="margin: 0;"> <span id="LC1473" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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1396
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<td class="diff-line-num new_line" data-linenumber="1474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1474
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<pre style="margin: 0;"> <span id="LC1474" class="line" lang="perl"> <span class="nv" style="color: teal;">$head</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$ignorehead</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1397
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1475
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<pre style="margin: 0;"> <span id="LC1475" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$ctrd</span><span class="p">,</span><span class="nv" style="color: teal;">$recruit_mate</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="nv" style="color: teal;">loadSequence</span><span class="p">(</span><span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$ctrd</span><span class="p">,</span><span class="nv" style="color: teal;">$sdna</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$head</span><span class="p">,</span><span class="nv" style="color: teal;">$up_iz</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$recruit_mate</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$sdna</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/^([ACGT]*)$/i</span><span class="p">);</span></span>
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1476
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<pre style="margin: 0;">+<span id="LC1476" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">####num</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1477" 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">
1477
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<pre style="margin: 0;">+<span id="LC1477" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$sdna</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1478" 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">
1478
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<pre style="margin: 0;">+<span id="LC1478" class="line" lang="perl"> <span class="nv" style="color: teal;">$sumall</span><span class="o" style="font-weight: 600;">+=</span><span class="nv" style="color: teal;">$len</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1479" 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">
1479
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<pre style="margin: 0;">+<span id="LC1479" class="line" lang="perl"> <span class="nv" style="color: teal;">$ctall</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1398
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1480
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<pre style="margin: 0;"> <span id="LC1480" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1399
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<td class="diff-line-num new_line" data-linenumber="1481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1481
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<pre style="margin: 0;"> <span id="LC1481" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="sr" style="color: #009926;">/^\>(\S+)/</span><span class="p">){</span></span>
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1400
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1482
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<pre style="margin: 0;"> <span id="LC1482" class="line" lang="perl"> <span class="nv" style="color: teal;">$head</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1422" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1422,7 +1504,7 @@ sub readFasta{</td>
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1422
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1504
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<pre style="margin: 0;"> <span id="LC1504" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">LOG</span> <span class="nv" style="color: teal;">$read_number_message</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1423" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1423
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1505
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<pre style="margin: 0;"> <span id="LC1505" class="line" lang="perl"> <span class="nv" style="color: teal;">$assemblyruninfo</span><span class="o" style="font-weight: 600;">.=</span><span class="nv" style="color: teal;">$read_number_message</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 old_line" data-linenumber="1424" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1424
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1506
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<pre style="margin: 0;"> <span id="LC1506" class="line" lang="perl"></span>
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1425
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<pre style="margin: 0;">-<span id="LC1425" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$matepair</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1426" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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1507
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<pre style="margin: 0;">+<span id="LC1507" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$set</span><span class="p">,</span><span class="nv" style="color: teal;">$bin</span><span class="p">,</span><span class="nv" style="color: teal;">$matepair</span><span class="p"><span class="idiff left">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$sumall</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$ctall</span></span><span class="p">;</span></span>
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1426
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1508
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<pre style="margin: 0;"> <span id="LC1508" class="line" lang="perl"><span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1427
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1509
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<pre style="margin: 0;"> <span id="LC1509" class="line" lang="perl"></span>
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<td class="diff-line-num old_line" data-linenumber="1428" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1428
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1510
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<pre style="margin: 0;"> <span id="LC1510" 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="1522" style="width: 35px; color: rgba(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="1604" style="width: 35px; color: rgba(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">@@ -1522,8 +1604,12 @@ sub loadSequence{</td>
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1522
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1604
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<pre style="margin: 0;"> <span id="LC1604" class="line" lang="perl"> <span class="nv" style="color: teal;">$set</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$orig</span><span class="p">}{</span><span class="s" style="color: #d14;">'count'</span><span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1523
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1605
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<pre style="margin: 0;"> <span id="LC1605" class="line" lang="perl"> <span class="nv" style="color: teal;">$set</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$orig</span><span class="p">}{</span><span class="s" style="color: #d14;">'names'</span><span class="p">}{</span><span class="nv" style="color: teal;">$head</span><span class="p">}</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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1524
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1606
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<pre style="margin: 0;"> <span id="LC1606" class="line" lang="perl"> <span class="nv" style="color: teal;">$set</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$orig</span><span class="p">}{</span><span class="s" style="color: #d14;">'grace'</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$up_iz</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1525" 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">
1525
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<td class="diff-line-num new_line old" data-linenumber="1607" 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="LC1525" class="line" lang="perl"> <span class="nv" style="color: teal;">$bin</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$orig</span><span class="p">}</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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1526
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<pre style="margin: 0;">-<span id="LC1526" class="line" lang="perl"> <span class="nv" style="color: teal;">$bin</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$rc</span><span class="p">}</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="1607" 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">
1607
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<pre style="margin: 0;">+<span id="LC1607" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1608
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<pre style="margin: 0;">+<span id="LC1608" class="line" lang="perl"> <span class="nv" style="color: teal;">$barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$head</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\_(\w+)/</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">### Jan 2018 THERE SHOULD ONLY BE ONE _ FOLLOWED BY BARCODE/INDEX/NUMBER</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1609" 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">
1609
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<pre style="margin: 0;">+<span id="LC1609" class="line" lang="perl"> <span class="nv" style="color: teal;">$bin</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$f</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$orig</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$barcode</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">### Jan 2018</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1610
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<pre style="margin: 0;">+<span id="LC1610" class="line" lang="perl"> <span class="nv" style="color: teal;">$bin</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$e</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$r</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]}}{</span><span class="nv" style="color: teal;">$rc</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$barcode</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">### Jan 2018</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1611" 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">
1611
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<pre style="margin: 0;">+<span id="LC1611" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#was $bin->{$e->{$f[0]}}{$e->{$f[1]}}{$e->{$f[2]}}{$e->{$f[3]}}{$orig}++;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1612" 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">
1612
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<pre style="margin: 0;">+<span id="LC1612" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#was $bin->{$e->{$r[0]}}{$e->{$r[1]}}{$e->{$r[2]}}{$e->{$r[3]}}{$rc}++;</span></span>
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1527
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1613
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<pre style="margin: 0;"> <span id="LC1613" class="line" lang="perl"> </span>
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<td class="diff-line-num old_line" data-linenumber="1528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1528
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1614
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<pre style="margin: 0;"> <span id="LC1614" class="line" lang="perl"> <span class="nv" style="color: teal;">$recruit_mate</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1529
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1615
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<pre style="margin: 0;"> <span id="LC1615" class="line" lang="perl"> <span class="nv" style="color: teal;">$ctrd</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1643" style="width: 35px; color: rgba(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="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1643,7 +1729,8 @@ sub forcefillGaps{</td>
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1643
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<td class="diff-line-num new_line" data-linenumber="1729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1729
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<pre style="margin: 0;"> <span id="LC1729" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">reverseComplement</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$orient</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"f"</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">###turn tig around for extension with previous reads</span></span>
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<td class="diff-line-num old_line" data-linenumber="1644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1644
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1730
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<pre style="margin: 0;"> <span id="LC1730" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$track</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1645
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<td class="diff-line-num new_line" data-linenumber="1731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1731
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<pre style="margin: 0;"> <span id="LC1731" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span><span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span><span class="nv" style="color: teal;">$tig_count</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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1646
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<td class="diff-line-num new_line old" data-linenumber="1732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1646" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_miniset</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_minibin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">doExtension</span><span class="p">(</span><span class="s" style="color: #d14;">"GAP left"</span><span class="p">,</span> <span class="nv" style="color: teal;">$MAX</span><span class="p">,</span> <span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_miniset</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_minibin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$base_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_base_ratio</span><span class="p">,</span> <span class="nv" style="color: teal;">$verbose</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p">,</span> <span class="nv" style="color: teal;">$forcetrack</span><span class="p">,</span> <span class="nv" style="color: teal;">$tig_count</span><span class="p">,</span> <span class="nv" style="color: teal;">$max_trim</span><span class="p">,</span> <span class="nv" style="color: teal;">$encoded</span><span class="p">,</span> <span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$tie_breaker</span><span class="p">,</span><span class="nv" style="color: teal;">$ignore_read</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$ct</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">###no need to extend first ($ct=0) contig on the left</span></span>
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1732
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<pre style="margin: 0;">+<span id="LC1732" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$barcodeList</span><span class="p">;</span></span>
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1733
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<pre style="margin: 0;">+<span id="LC1733" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_miniset</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_minibin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p">,</span> <span class="nv" style="color: teal;">$barcodeList</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">doExtension</span><span class="p">(</span><span class="s" style="color: #d14;">"GAP left"</span><span class="p">,</span> <span class="nv" style="color: teal;">$MAX</span><span class="p">,</span> <span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_miniset</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_minibin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$base_overlap</span><span class="p">,</span> <span class="nv" style="color: teal;">$min_base_ratio</span><span class="p">,</span> <span class="nv" style="color: teal;">$verbose</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p">,</span> <span class="nv" style="color: teal;">$forcetrack</span><span class="p">,</span> <span class="nv" style="color: teal;">$tig_count</span><span class="p">,</span> <span class="nv" style="color: teal;">$max_trim</span><span class="p">,</span> <span class="nv" style="color: teal;">$encoded</span><span class="p">,</span> <span class="nv" style="color: teal;">$matepair</span><span class="p">,</span><span class="nv" style="color: teal;">$tie_breaker</span><span class="p">,</span><span class="nv" style="color: teal;">$ignore_read</span><span class="p">,</span><span class="nv" style="color: teal;">$barcodeList</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$ct</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">###no need to extend first ($ct=0) contig on the left</span></span>
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1647
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1734
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<pre style="margin: 0;"> <span id="LC1734" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$prev_miniset</span><span class="p">,</span> <span class="nv" style="color: teal;">$prev_minibin</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="p">({},{});</span></span>
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1648
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1735
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<pre style="margin: 0;"> <span id="LC1735" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">reverseComplement</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">###re-change orientation for right extension (both fwd/rev tigs)</span></span>
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1649
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1736
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<pre style="margin: 0;"> <span id="LC1736" class="line" lang="perl"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1758" style="width: 35px; color: rgba(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">@@ -1758,7 +1845,7 @@ sub forcefillGaps{</td>
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1758
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1845
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<pre style="margin: 0;"> <span id="LC1845" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$up_iz</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$collect_candidates</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$mateseq</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$min_allowed</span><span class="p">;</span></span>
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1759
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<td class="diff-line-num new_line" data-linenumber="1846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1846
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<pre style="margin: 0;"> <span id="LC1846" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$miniset</span><span class="p">,</span><span class="nv" style="color: teal;">$minibin</span><span class="p">,</span><span class="nv" style="color: teal;">$ctrd</span><span class="p">,</span><span class="nv" style="color: teal;">$recruit_mate</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;">loadSequence</span><span class="p">(</span><span class="nv" style="color: teal;">$miniset</span><span class="p">,</span><span class="nv" style="color: teal;">$minibin</span><span class="p">,</span><span class="nv" style="color: teal;">$ctrd</span><span class="p">,</span><span class="nv" style="color: teal;">$mateseq</span><span class="p">,</span><span class="nv" style="color: teal;">$encoded</span><span class="p">,</span><span class="nv" style="color: teal;">$head</span><span class="p">,</span><span class="nv" style="color: teal;">$up_iz</span><span class="p">,</span><span class="nv" style="color: teal;">$seedsplit</span><span class="p">,</span><span class="nv" style="color: teal;">$space_restriction</span><span class="p">,</span><span class="nv" style="color: teal;">$targetwordlen</span><span class="p">,</span><span class="nv" style="color: teal;">$recruit_mate</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$mateseq</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="nv" style="color: teal;">$illuminaLengthCutoff</span><span class="p">);</span></span>
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1760
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1847
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<pre style="margin: 0;"> <span id="LC1847" class="line" lang="perl"> <span class="p">}</span></span>
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1761
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<pre style="margin: 0;">-<span id="LC1761" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$miniset</span><span class="p">,</span> <span class="nv" style="color: teal;">$minibin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p"><span class="idiff left">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">doExtension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"GAP right"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$MAX</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$miniset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$minibin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$reads_needed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$total_bases</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$base_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_base_ratio</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$verbose</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$track</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$forcetrack</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$tig_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$max_trim</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$encoded</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$matepair</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$tie_breaker</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$ignore_read</span></span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">### extend first contig on the right</span></span>
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1848
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<pre style="margin: 0;">+<span id="LC1848" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">,</span> <span class="nv" style="color: teal;">$miniset</span><span class="p">,</span> <span class="nv" style="color: teal;">$minibin</span><span class="p">,</span> <span class="nv" style="color: teal;">$reads_needed</span><span class="p">,</span> <span class="nv" style="color: teal;">$total_bases</span><span class="p">,</span> <span class="nv" style="color: teal;">$track</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$barcodeList</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">doExtension</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"GAP right"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$MAX</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$miniset</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$minibin</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$reads_needed</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$total_bases</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$base_overlap</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$min_base_ratio</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$verbose</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$track</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$forcetrack</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$tig_count</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$max_trim</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$encoded</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nv" style="color: teal;"><span class="idiff">$matepair</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$tie_breaker</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff">$ignore_read</span></span><span class="p"><span class="idiff">,</span></span><span class="nv" style="color: teal;"><span class="idiff right">$barcodeList</span></span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">### extend first contig on the right</span></span>
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1762
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1849
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<pre style="margin: 0;"> <span id="LC1849" class="line" lang="perl"> <span class="nv" style="color: teal;">$prev_miniset</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$miniset</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">###used reads have been deleted</span></span>
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1763
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1850
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<pre style="margin: 0;"> <span id="LC1850" class="line" lang="perl"> <span class="nv" style="color: teal;">$prev_minibin</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$minibin</span><span class="p">;</span></span>
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1764
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1851
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<pre style="margin: 0;"> <span id="LC1851" class="line" lang="perl"> <span class="p">(</span><span class="nv" style="color: teal;">$miniset</span><span class="p">,</span><span class="nv" style="color: teal;">$minibin</span><span class="p">)</span><span class="o" style="font-weight: 600;">=</span><span class="p">({},{});</span><span class="c1" style="color: #998; font-style: italic;">### flush custom prefix tree minibin and miniset</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1850" style="width: 35px; color: rgba(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="1937" style="width: 35px; color: rgba(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">@@ -1850,4 +1937,121 @@ sub forcefillGaps{</td>
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1850
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1937
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<pre style="margin: 0;"> <span id="LC1937" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">OUT</span><span class="p">;</span></span>
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1851
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1938
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<pre style="margin: 0;"> <span id="LC1938" class="line" lang="perl"><span class="p">}</span></span>
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1852
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1939
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<pre style="margin: 0;"> <span id="LC1939" class="line" lang="perl"></span>
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1940
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<pre style="margin: 0;">+<span id="LC1940" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#-------------------</span></span>
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1941
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<pre style="margin: 0;">+<span id="LC1941" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">readContigsMemory</span><span class="p">{</span></span>
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1942
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<pre style="margin: 0;">+<span id="LC1942" 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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1943
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<pre style="margin: 0;">+<span id="LC1943" class="line" lang="perl"></span>
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1944
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<pre style="margin: 0;">+<span id="LC1944" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tig_length</span><span class="p">;</span></span>
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1945
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<pre style="margin: 0;">+<span id="LC1945" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tignames</span><span class="p">;</span></span>
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1946
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<pre style="margin: 0;">+<span id="LC1946" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$fh</span><span class="p">;</span></span>
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1947
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<pre style="margin: 0;">+<span id="LC1947" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$prevhead</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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1948
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<pre style="margin: 0;">+<span id="LC1948" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seq</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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1949
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<pre style="margin: 0;">+<span id="LC1949" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$cttig</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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1950
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<pre style="margin: 0;">+<span id="LC1950" class="line" lang="perl"></span>
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1951
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<pre style="margin: 0;">+<span id="LC1951" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">###Support for compressed files MAR2016</span></span>
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1952
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<pre style="margin: 0;">+<span id="LC1952" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$file</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/zip$/i</span><span class="p">){</span></span>
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1953
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<pre style="margin: 0;">+<span id="LC1953" 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;">"unzip -p $file|"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Error reading $file -- fatal\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1954" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1954
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<pre style="margin: 0;">+<span id="LC1954" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">elsif</span><span class="p">(</span><span class="nv" style="color: teal;">$file</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/gz$/i</span> <span class="o" style="font-weight: 600;">||</span> <span class="nv" style="color: teal;">$file</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/gzip$/i</span><span class="p">){</span></span>
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1955
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<pre style="margin: 0;">+<span id="LC1955" 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;">"gunzip -c $file|"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Error reading $file -- fatal\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1956" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1956
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<pre style="margin: 0;">+<span id="LC1956" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1957" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1957
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<pre style="margin: 0;">+<span id="LC1957" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">IN</span><span class="p">,</span><span class="nv" style="color: teal;">$file</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Error reading $file -- fatal\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1958" 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">
1958
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<pre style="margin: 0;">+<span id="LC1958" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1959" 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">
1959
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<pre style="margin: 0;">+<span id="LC1959" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1960" 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">
1960
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<pre style="margin: 0;">+<span id="LC1960" 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>
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<td class="diff-line-num new new_line" data-linenumber="1961" 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">
1961
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<pre style="margin: 0;">+<span id="LC1961" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1962" 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">
1962
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<pre style="margin: 0;">+<span id="LC1962" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="sr" style="color: #009926;">/^\>(.*)/</span><span class="p">){</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1963" 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">
1963
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<pre style="margin: 0;">+<span id="LC1963" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$head</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1964" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1964
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<pre style="margin: 0;">+<span id="LC1964" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1965" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1965
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<pre style="margin: 0;">+<span id="LC1965" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: teal;">$head</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="nv" style="color: teal;">$prevhead</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$seq</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">''</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$prevhead</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">''</span><span class="p">){</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1966" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1966
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<pre style="margin: 0;">+<span id="LC1966" class="line" lang="perl"> <span class="nv" style="color: teal;">$cttig</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1967" 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">
1967
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<pre style="margin: 0;">+<span id="LC1967" class="line" lang="perl"> <span class="nv" style="color: teal;">$tignames</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$cttig</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$prevhead</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1968" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1968
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<pre style="margin: 0;">+<span id="LC1968" class="line" lang="perl"> <span class="nv" style="color: teal;">$fh</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$cttig</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$seq</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1969" 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">
1969
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<pre style="margin: 0;">+<span id="LC1969" class="line" lang="perl"> <span class="nv" style="color: teal;">$tig_length</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$cttig</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1970" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1970
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<pre style="margin: 0;">+<span id="LC1970" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1971" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1971
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1971" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1972" 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">
1972
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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="LC1972" class="line" lang="perl"> <span class="nv" style="color: teal;">$prevhead</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$head</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1973" 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">
1973
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<pre style="margin: 0;">+<span id="LC1973" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1974" 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">
1974
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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="LC1974" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nb" style="color: #0086b3;">uc</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="p">);</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1975" 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">
1975
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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="LC1975" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1976" 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">
1976
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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="LC1976" class="line" lang="perl"> <span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1977" 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">
1977
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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="LC1977" class="line" lang="perl"> <span class="nv" style="color: teal;">$cttig</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1978
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<pre style="margin: 0;">+<span id="LC1978" class="line" lang="perl"> <span class="nv" style="color: teal;">$tignames</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$cttig</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$prevhead</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1979" 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">
1979
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<pre style="margin: 0;">+<span id="LC1979" class="line" lang="perl"> <span class="nv" style="color: teal;">$fh</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$cttig</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$seq</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1980
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<pre style="margin: 0;">+<span id="LC1980" class="line" lang="perl"> <span class="nv" style="color: teal;">$tig_length</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$cttig</span><span class="p">}</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1981" 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">
1981
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<pre style="margin: 0;">+<span id="LC1981" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1982" 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">
1982
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<pre style="margin: 0;">+<span id="LC1982" class="line" lang="perl"> <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: teal;">$fh</span><span class="p">,</span><span class="nv" style="color: teal;">$tignames</span><span class="p">,</span><span class="nv" style="color: teal;">$tig_length</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1983" 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">
1983
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<pre style="margin: 0;">+<span id="LC1983" class="line" lang="perl"><span class="p">}</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1984" 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">
1984
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<pre style="margin: 0;">+<span id="LC1984" class="line" lang="perl"></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1985" 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">
1985
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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="LC1985" class="line" lang="perl"></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="1986" 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">
1986
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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="LC1986" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#-------------------</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1987" 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">
1987
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<pre style="margin: 0;">+<span id="LC1987" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">buildScaffoldFasta</span><span class="p">{</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="1988" 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">
1988
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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="LC1988" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1989" 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">
1989
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<pre style="margin: 0;">+<span id="LC1989" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: teal;">$dotscaffold</span><span class="p">,</span><span class="nv" style="color: teal;">$fh</span><span class="p">,</span><span class="nv" style="color: teal;">$scaffold_fasta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">@_</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1990" 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">
1990
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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="LC1990" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1991" 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">
1991
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1991" 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="nv" style="color: teal;">$dotscaffold</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"Cannot open $dotscaffold for reading -- fatal.\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1992
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1992" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1993
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1993" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nv" style="color: teal;">OUT</span><span class="p">,</span><span class="s" style="color: #d14;">">$scaffold_fasta"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">die</span> <span class="s" style="color: #d14;">"can't write to $scaffold_fasta -- fatal\n"</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1994
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1994" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1995
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1995" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tot</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1996" 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">
1996
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1996" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$ct</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="1997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1997
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1997" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$sct</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1998" 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">
1998
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1998" 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="c1" style="color: #998; font-style: italic;">### each line</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="1999" 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">
1999
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1999" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">chomp</span><span class="p">;</span> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2000" 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">
2000
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<pre style="margin: 0;">+<span id="LC2000" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$sc</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 new new_line" data-linenumber="2001" 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">
2001
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<pre style="margin: 0;">+<span id="LC2001" 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><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2002" 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">
2002
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<pre style="margin: 0;">+<span id="LC2002" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">@tig</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2003" 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">
2003
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<pre style="margin: 0;">+<span id="LC2003" class="line" lang="perl"> </span>
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<td class="diff-line-num new new_line" data-linenumber="2004" 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">
2004
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<pre style="margin: 0;">+<span id="LC2004" 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="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/\_/</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2005" 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">
2005
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<pre style="margin: 0;">+<span id="LC2005" class="line" lang="perl"> <span class="nv" style="color: teal;">@tig</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><span class="p">,</span><span class="nv" style="color: teal;">$a</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2006" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2006
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<pre style="margin: 0;">+<span id="LC2006" class="line" lang="perl"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2007" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2007
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<pre style="margin: 0;">+<span id="LC2007" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span> <span class="nv" style="color: teal;">@tig</span><span class="p">,</span> <span class="nv" style="color: teal;">$a</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="2008" 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">
2008
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<pre style="margin: 0;">+<span id="LC2008" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2009" 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">
2009
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<pre style="margin: 0;">+<span id="LC2009" class="line" lang="perl"></span>
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<td class="diff-line-num new new_line" data-linenumber="2010" 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">
2010
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<pre style="margin: 0;">+<span id="LC2010" class="line" lang="perl"> <span class="nv" style="color: teal;">$sct</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2011" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2011
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<pre style="margin: 0;">+<span id="LC2011" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tigsum</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="2012" 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">
2012
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<pre style="margin: 0;">+<span id="LC2012" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">OUT</span> <span class="s" style="color: #d14;">">$_\n"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2013" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2013
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<pre style="margin: 0;">+<span id="LC2013" class="line" lang="perl"> <span class="k" style="font-weight: 600;">foreach</span> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$t</span> <span class="p">(</span><span class="nv" style="color: teal;">@tig</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2014" 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">
2014
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<pre style="margin: 0;">+<span id="LC2014" class="line" lang="perl"> <span class="nv" style="color: teal;">$ct</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2015" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2015
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<pre style="margin: 0;">+<span id="LC2015" class="line" lang="perl"> </span>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2016" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2016
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<pre style="margin: 0;">+<span id="LC2016" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$t</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/([fr])(\d+)z(\d+)(\S+)?/i</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2017" 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">
2017
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<pre style="margin: 0;">+<span id="LC2017" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2018" 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">
2018
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<pre style="margin: 0;">+<span id="LC2018" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$orient</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2019" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2019
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<pre style="margin: 0;">+<span id="LC2019" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$tnum</span><span class="o" style="font-weight: 600;">=</span><span class="nv" style="color: teal;">$2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2020" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2020
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<pre style="margin: 0;">+<span id="LC2020" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$head</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$orient</span> <span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: teal;">$tnum</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2021" 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">
2021
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<pre style="margin: 0;">+<span id="LC2021" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$search</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$tnum</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2022" 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">
2022
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<pre style="margin: 0;">+<span id="LC2022" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$other</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$4</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2023
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<pre style="margin: 0;">+<span id="LC2023" class="line" lang="perl"> <span class="nv" style="color: teal;">$tot</span><span class="o" style="font-weight: 600;">+=</span> <span class="nv" style="color: teal;">$3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2024" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2024
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<pre style="margin: 0;">+<span id="LC2024" class="line" lang="perl"> <span class="nv" style="color: teal;">$tigsum</span> <span class="o" style="font-weight: 600;">+=</span><span class="nv" style="color: teal;">$3</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2025
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<pre style="margin: 0;">+<span id="LC2025" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2026
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<pre style="margin: 0;">+<span id="LC2026" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NA"</span><span class="p">;</span> </span>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="2027" 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">
2027
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<pre style="margin: 0;">+<span id="LC2027" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$numlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NA"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2028
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<pre style="margin: 0;">+<span id="LC2028" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$linksratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NA"</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="2029" 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">
2029
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<pre style="margin: 0;">+<span id="LC2029" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="2030" 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">
2030
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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$gapseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2031
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<pre style="margin: 0;">+<span id="LC2031" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2032
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<pre style="margin: 0;">+<span id="LC2032" class="line" lang="perl"> <span class="nv" style="color: teal;">$numlinks</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$other</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/k(\d+)/</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="2033" 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">
2033
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<pre style="margin: 0;">+<span id="LC2033" class="line" lang="perl"> <span class="nv" style="color: teal;">$linksratio</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$other</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/a(\d+.*)m/</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="2034" 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">
2034
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<pre style="margin: 0;">+<span id="LC2034" class="line" lang="perl"> <span class="nv" style="color: teal;">$gap</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$1</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$other</span><span class="o" style="font-weight: 600;">=~</span><span class="sr" style="color: #009926;">/m(\-?\d+)/</span><span class="p">);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="2035" 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">
2035
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<pre style="margin: 0;">+<span id="LC2035" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" 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="2036" 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">
2036
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<pre style="margin: 0;">+<span id="LC2036" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$fh</span><span class="o" style="font-weight: 600;">-></span><span class="p">{</span><span class="nv" style="color: teal;">$search</span><span class="p">};</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1853" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="2037" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2037
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<pre style="margin: 0;">+<span id="LC2037" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">reverseComplement</span><span class="p">(</span><span class="nv" style="color: teal;">$seq</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$orient</span> <span class="ow" style="font-weight: 600;">eq</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2038" 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">
2038
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<pre style="margin: 0;">+<span id="LC2038" class="line" lang="perl"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2039" 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">
2039
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<pre style="margin: 0;">+<span id="LC2039" class="line" lang="perl"> <span class="nv" style="color: teal;">$gapseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"N"</span> <span class="nv" style="color: teal;">x</span> <span class="nv" style="color: teal;">$gap</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$gap</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="2040" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2040
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<pre style="margin: 0;">+<span id="LC2040" class="line" lang="perl"> <span class="nv" style="color: teal;">$gapseq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"n"</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="nv" style="color: teal;">$gap</span> <span class="ow" style="font-weight: 600;">ne</span> <span class="s" style="color: #d14;">"NA"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nv" style="color: teal;">$gap</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span> <span class="p">);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2041" 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">
2041
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<pre style="margin: 0;">+<span id="LC2041" class="line" lang="perl"> <span class="nv" style="color: teal;">$seq</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$gapseq</span><span class="p">;</span></span>
</pre>
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2042
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<pre style="margin: 0;">+<span id="LC2042" class="line" lang="perl"></span>
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2043
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<pre style="margin: 0;">+<span id="LC2043" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">OUT</span> <span class="s" style="color: #d14;">"$seq"</span><span class="p">;</span> </span>
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2044
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<pre style="margin: 0;">+<span id="LC2044" class="line" lang="perl"> </span>
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<pre style="margin: 0;">+<span id="LC2045" class="line" lang="perl"> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">#tig regex</span></span>
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2046
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<pre style="margin: 0;">+<span id="LC2046" class="line" lang="perl"> </span>
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2047
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<pre style="margin: 0;">+<span id="LC2047" class="line" lang="perl"> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">#each tig</span></span>
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2048
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<pre style="margin: 0;">+<span id="LC2048" class="line" lang="perl"> <span class="k" style="font-weight: 600;">print</span> <span class="nv" style="color: teal;">OUT</span> <span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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2049
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<pre style="margin: 0;">+<span id="LC2049" class="line" lang="perl"> <span class="p">}</span></span>
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2050
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<pre style="margin: 0;">+<span id="LC2050" class="line" lang="perl"></span>
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2051
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<pre style="margin: 0;">+<span id="LC2051" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">CORROUT</span><span class="p">;</span></span>
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2052
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<pre style="margin: 0;">+<span id="LC2052" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">IN</span><span class="p">;</span></span>
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2053
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<pre style="margin: 0;">+<span id="LC2053" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">close</span> <span class="nv" style="color: teal;">OUT</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC2054" class="line" lang="perl"></span>
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<pre style="margin: 0;">+<span id="LC2055" class="line" lang="perl"><span class="p">}</span></span>
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2056
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<pre style="margin: 0;">+<span id="LC2056" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC2057" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">## We hope this code is useful to you -- Please send comments & suggestions to rwarren at bcgsc.ca</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) </span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="p"><span class="idiff left">![</span></span><span class="nv" style="color: teal;"><span class="idiff">Logo</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/warrenlr/ssake/blob/master/ssake-logo.png</span></span><span class="p"><span class="idiff right">)</span></span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">SSAKE v3.8.5 Rene L. Warren, 2006-2017</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">email: rwarren at bcgsc.ca</span>
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5
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;"># SSAKE</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Short Sequence Assembly by K-mer search and 3' read Extension</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## SSAKE v4.0 Rene L. Warren, 2006-2018</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## email: rwarren [at] bcgsc [dot] ca</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Visit www.bcgsc.ca/bioinfo/software/ssake for additional information</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Description</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gh" style="color: #999;">### Description</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gh" style="color: #999;">-----------</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences.</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown">It is an easy-to-use, robust, reliable and tractable assembly algorithm for short sequence reads, such as those generated by Illumina Ltd. </span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">For best performance</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>For best performance</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">Best assembly results are achieved with quality-trimmed reads. When dealing with Solexa/Illumina sequences, remove low quality bases, whenever possible, with:</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">TQS.py -f _seq.txt -q _prb.txt -t 5 -d 5 -l #CYCLES -c 20 OR OTHER SETTINGS </span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">TQSfastq.py -f myfile.fq -t 20 -c 30 -e 64</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">example:</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">~/ssake_v3.8.5/tools/TQSfastq.py -f ../myIlluminaSeqLane_1.fq -c 30 -t 20 ##mate no.1</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">~/ssake_v3.8.5/tools/TQSfastq.py -f ../myIlluminaSeqLane_2.fq -c 30 -t 20 ##mate no.2</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">~/ssake_v3.8.5/tools/makePairedOutput2UNEQUALfiles.pl ../myIlluminaSeqLane_1.fq_T20C20E64.trim.fa ../myIlluminaSeqLane_2.fq_T20C20E64.trim.fa</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown">~/ssake_v4.0/tools/</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown">TQS.py </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown">eg. TQS.py -f _seq.txt -q _prb.txt -t 5 -d 5 -l #CYCLES -c 20 OR OTHER SETTINGS </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown">TQSfastq.py</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown">eg. TQSfastq.py -f myfile.fq -t 20 -c 30 -e 64</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">TQSfastq.pl</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">eg. TQSfastq.pl -f human.fof -q 20 -n 70 -e 33</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">where human.fof contains fastq files to trim</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown">make sure the trimmed fastq ends with 1 and 2 for the first and second reads of a pair</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown">eg. makePairedOutput2UNEQUALfiles.pl NA24143_genome_phased_namesorted.bam1_1.fqc70q20e33.fa NA24143_genome_phased_namesorted.bam1_2.fqc70q20e33.fa 350</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown">will produced "paired.fa" and "unpaired.fa"</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">~/ssake_v3.8.5/SSAKE -f paired.fa -g unpaired.fa -p 1 -m 17 -o 4 -c 1 -w 5</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">~/ssake_v4.0/SSAKE -f paired.fa -g unpaired.fa -p 1 -m 20 -o 3 -c 1 -w 5</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown">A BASIC PIPELINE TO HELP YOU PREPARE YOUR INPUT PAIRED READS EXISTS (./tools/runSSAKE.sh)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown">USAGE: ./runSSAKE.sh read1.fq read2.fq libraryFragmentLength basename</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown">The scripts are located in ./tools subdirectory included with this release.</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="markdown">It is recommended that you run TQS.py/TQSfastq.py for every tile (batch job) and cat the outputted fasta file, especially if your data set is large (e.g. entire flowcell)</span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown">For trimming paired-end sequences (using _seq.txt and _prb.txt from Illumina), please refer to TRIMMING_PAIRED_READS.README located in the ./tools subdirectory</span>
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33
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">What's new in v3.8.5 ?</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v4.0 ?</span></span>
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36
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">Implements targeted de novo assembly. Fixed a bug that manifested when running SSAKE in targeted (-s) de novo assembly mode. Contig sequences as long as the seed sequence were previously misclassified as singlets. (thanks Gilberto Vaughan for reporting)</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">What's new in v3.8.4 ?</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown">-Initial support for linked reads, such as those produced by the 10x Genomics Chromium technology</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown">-Linked reads are supplied in the original SSAKE format, but the barcode information is indicated by sequence following a single underscore "_"</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">-Added a C. elegans linked read data assembly script in the test folder</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown">-Scaffolding options consistent with that of the LINKS scaffolder</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">-SSAKE no longer sorts by/prioritizes high multiplicity reads for assembly</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown">-Streamlined file names</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">-Deprecated force-fill gap feature</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">-Bug fixes</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.8.5 ?</span></span>
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42
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">Implements targeted de novo assembly. Fixed a bug that manifested when running SSAKE in targeted (-s) de novo assembly mode. Contig sequences as long as the seed sequence were previously misclassified as singlets.</span>
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65
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.8.4 ?</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown">Improvements to the targeted assembly functionality, recruiting whole read pairs for de novo assembly when at least one read has a k-mer match. This has the potential to extend the reconstructed contigs by 2X the library fragment size (upstream and downstream) of the target sequence when run in targeted de novo assembly mode -s and -i 1 (default).</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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45
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">What's new in v3.8.3 ?</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.8.3 ?</span></span>
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48
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown">Included tie-breaker option (-q) when determining consensus from equal-coverage bases. When set (-q 1), the parameter r is overridden. Note that even though the base is "randomly" chosen in such situations, SSAKE will only extend contigs in cases where there is read support over the chosen base. Included option to ignore reads making up the consensus base extension (-y).</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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49
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">Included tie-breaker option (-q) when determining consensus from equal-coverage bases. When set (-q 1), the parameter r is overridden. Note that even though a "random" base is chosen in such situations, SSAKE will only extend contigs in cases where there is read supportover the chosen base. Included option to ignore reads making up the consensus base extension (-y).</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"></span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">What's new in v3.8.2 ?</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.8.2 ?</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="markdown">Included target word length (-j option) - TASR behaviour (equivalent to -k option in TASR)</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">What's new in v3.8.1 ?</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.8.1 ?</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="gh" style="color: #999;">----------------------</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown">fixed SSAKE for Perl >= 5.16.0, where deprecated getopts.pl has been removed. Thanks to Nicola Soranzo for sending the fix.</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">What's new in v3.8+ ?</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.8+ ?</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">This release is 30% faster than v3.7, made possible by 4-base encoding of the first 16 bases of each read while populating a 4-nodes (16/4) prefix tree. Also, the newly implemented (and required) -w option, gives users more control over the assembly, focusing on higher-depth contigs and ignoring short, low-depth contigs comprised of NGS reads having errors, contaminating reads or any other (perhaps unwanted) sequences. </span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>The assembly of 25M high-quality (100bp x 2 x Q30) bacterial NGS reads (1 lane, Illumina HiSeq) with SSAKE v3.7 in single-end mode took 2h50. SSAKE v3.8 ran for 2h on the same data. A SSAKE v3.8 assembly restricted to high-depth contigs (-w 10) ran in 33 minutes, and eliminated thousands of short, low depth of coverage contigs that would otherwise arise from contaminating reads and reads with base errors. </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">@@ -75,6 +101,7 @@ Campylobacter showae CC57C colorectal cancer tumor isolate (~2Mbp genome) Illumi</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown">ftp://ftp.bcgsc.ca/supplementary/SSAKE/CC57C_paired.fa and CC57C_unpaired.fa</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"> </span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown">SSAKE ASSEMBLY PIPELINE:</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown">./test/runSSAKE.sh</span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown">./tools/TQSfastq.py -f Assemble_1_R1.fastq -t 30 -c 100 -e 33</span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="markdown">./tools/TQSfastq.py -f Assemble_1_R2.fastq -t 30 -c 100 -e 33</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">@@ -82,125 +109,82 @@ cat Assemble_1_R2.fastq_T30C100E33.trim.fa |perl -ne 'if(/^(\>\@\S+)/){print "$1</td>
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82
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown">cat Assemble_1_R1.fastq_T30C100E33.trim.fa |perl -ne 'if(/^(<span class="se" style="color: #d14;">\>\@\S</span>+)/){print "$1a<span class="se" style="color: #d14;">\n</span>";}else{print;}' >Assemble_1_R1.fastq_T30C100E33.trimFIX.fa</span>
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83
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="markdown">./tools/makePairedOutput2UNEQUALfiles.pl Assemble_1_R1.fastq_T30C100E33.trimFIX.fa Assemble_1_R2.fastq_T30C100E33.trimFIX.fa 400</span>
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84
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown">./Syrupy-1.4.0/scripts/syrupy.py ./SSAKE -f CC57C_paired.fa -p 1 -g CC57C_unpaired.fa -m 20 -w 5 -b run2014</span>
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85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="plaintext"></span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">./ssake_v<span class="idiff left right">3.8.5/tools/getStats.pl run2014.contigs</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown">./ssake_v4.0/tools/getStats.pl run2014_contigs.fa</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown">./ssake_v<span class="idiff left right">4.0/tools/getStats.pl run2014_scaffolds.fa</span></span>
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87
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"></span>
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88
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown">TRY IT OUT BY SIMPLY RUNNING:</span>
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89
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="markdown"></span>
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90
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown">cd test;./MiSeqCampylobacterAssemblyPIPELINE.sh</span>
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91
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown">cd test;./MiSeqCampylobacterAssembly.sh</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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92
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"></span>
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93
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="plaintext">CONTIG SEQUENCE STATS</span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="plaintext">--------------------------------------------------------------------------------</span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">Mean (nt),10476.89</span>
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97
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="plaintext">Max (nt),119107</span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext">Min (nt),200</span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext">n,215</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="100" 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">
100
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC100" class="line" lang="plaintext">Stdev (nt),19021.54</span>
</pre>
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</tr>
<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="101" 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">
101
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC101" class="line" lang="plaintext">Variance (nt),361818996.83</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="102" 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">
102
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC102" class="line" lang="plaintext">TrimmedMean (nt),2763.44</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="103" 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">
103
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC103" class="line" lang="plaintext">Median (nt),412.00</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="104" 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">
104
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<td class="diff-line-num new_line old" data-linenumber="122" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext">Sum (nt),2252531.00</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="105" 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">
105
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<td class="diff-line-num new_line old" data-linenumber="122" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">N20,64969</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="106" 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">
106
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<td class="diff-line-num new_line old" data-linenumber="122" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext">N50,41436</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="107" 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">
107
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC107" class="line" lang="plaintext">N80,17465</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="108" 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">
108
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC108" class="line" lang="plaintext">Size Range,#bases,#sequences</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="109" 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">
109
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC109" class="line" lang="plaintext">>=100000,119107,1</span>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="110" 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">
110
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC110" class="line" lang="plaintext">10000-100000,1951445,63</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="111" 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">
111
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC111" class="line" lang="plaintext">200-1000,36330,119</span>
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<td class="diff-line-num old old_line" data-linenumber="112" 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">
112
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC112" class="line" lang="plaintext">1000-10000,145649,32</span>
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<td class="diff-line-num old old_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="plaintext">./ssake_v3.8.5/tools/makeFastaFileFromScaffolds.pl run2014.scaffolds</span>
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<td class="diff-line-num old old_line" data-linenumber="115" 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">
115
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC115" class="line" lang="plaintext">./ssake_v3.8.5/tools/getStats.pl run2014.scaffolds.fa</span>
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<td class="diff-line-num old old_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
117
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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="plaintext">SCAFFOLD SEQUENCE STATS</span>
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<td class="diff-line-num old old_line" data-linenumber="118" 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">
118
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC118" class="line" lang="plaintext">--------------------------------------------------------------------------------</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
119
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<td class="diff-line-num new_line old" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">Mean (nt),14931.05</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="120" 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">
120
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC120" class="line" lang="plaintext">Max (nt),252560</span>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
121
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC121" class="line" lang="plaintext">Min (nt),200</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="122" 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">
122
</td>
<td class="diff-line-num new_line old" data-linenumber="122" 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">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC122" class="line" lang="plaintext">n,151</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="123" 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">
123
</td>
<td class="diff-line-num new_line old" data-linenumber="122" 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">
</td>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext">Stdev (nt),42086.22</span>
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<td class="diff-line-num old old_line" data-linenumber="124" 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">
124
</td>
<td class="diff-line-num new_line old" data-linenumber="122" 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="LC124" class="line" lang="plaintext">Variance (nt),1771250106.52</span>
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<td class="diff-line-num old old_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="plaintext">TrimmedMean (nt),349.95</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="126" 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">
126
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC126" class="line" lang="plaintext">Median (nt),288.00</span>
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<td class="diff-line-num old old_line" data-linenumber="127" 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">
127
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC127" class="line" lang="plaintext">Sum (nt),2254589.00</span>
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128
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC128" class="line" lang="plaintext">N20,227805</span>
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<td class="diff-line-num old old_line" data-linenumber="129" 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">
129
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC129" class="line" lang="plaintext">N50,124387</span>
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<td class="diff-line-num old old_line" data-linenumber="130" 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">
130
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<td class="diff-line-num new_line old" data-linenumber="122" 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="LC130" class="line" lang="plaintext">N80,59173</span>
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<td class="diff-line-num old old_line" data-linenumber="131" 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">
131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="plaintext">Size Range,#bases,#sequences</span>
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<td class="diff-line-num old old_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="plaintext">>=100000,1350704,8</span>
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<td class="diff-line-num old old_line" data-linenumber="133" 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">
133
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<td class="diff-line-num new_line old" data-linenumber="122" 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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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC133" class="line" lang="plaintext">10000-100000,805378,18</span>
</pre>
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<tr class="line_holder old" id="" style="line-height: 1.6;">
<td class="diff-line-num old old_line" data-linenumber="134" 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">
134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="plaintext">200-1000,33684,113</span>
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<td class="diff-line-num old old_line" data-linenumber="135" 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">
135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="plaintext">1000-10000,63291,12</span>
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<td class="diff-line-num old old_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="137" 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">
137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="138" 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">
138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="plaintext">What's new in v3.7+ ?</span>
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<td class="diff-line-num new old_line" data-linenumber="139" 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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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.7+ ?</span></span>
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139
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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<td class="diff-line-num old old_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_line" data-linenumber="141" 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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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<td class="diff-line-num old_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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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="markdown">v3.7+ Improved support for seed-based -s assemblies, notably read-space restriction option -u (TASR behavior, without fastq support)</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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142
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="144" 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">
144
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="plaintext">What's new in v3.6+ ?</span>
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<td class="diff-line-num new old_line" data-linenumber="145" 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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.6+ ?</span></span>
</pre>
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<td class="diff-line-num 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">
145
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129
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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="LC129" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown">v3.6+ supports various insert size sequence libraries. To work with paired data, users must add ":insert_size" (e.g. >SLXA23-1-1-2-13:200 for a 200bp library) at the end of the fasta header (>) for each pairs. v3.6 also has preliminary support for Sanger, paired-end reads.</span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="plaintext">What's new in v3.5+ ?</span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.5+ ?</span></span>
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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153
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="markdown">In v3.5, the read pairing logic is used in the extension process. More specifically, passed the upper bound insert size, only forward reads AND reverse reads having their assembled mate already assembled in the contig being built will be considered for extension. This has for effect to mitigate contig misassemblies due to repeats. It will also extend the end of adjacent contigs in a scaffold in an effort to fill gaps - the resulting contigs are placed in the .mergedcontigs file.</span>
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138
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="plaintext">What's new in v3.4+ ?</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.4+ ?</span></span>
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157
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="markdown">Version 3.4 exploits paired-end reads to explore possible contig merges within scaffolds (Consecutive contigs >= -z bases must overlap by -m bases or more). Version v3.4.1 allows a user to merge all contigs of a scaffold by padding predicted gaps with Ns (-n 1) and predicted but undetected overlaps with a single (n). Merged contigs are outputted in the _mergedcontigs.fa file. The default behaviour (-n 0) is to NOT pad the gaps with Ns (v3.4 behaviour). In the v3.4.1, the _readposition.txt file tracks read names instead of read sequences as the latter can be inferred from the start and end coordinates. THIS IS NOW (v4.0) DEPRECATED.</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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158
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"></span>
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159
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="plaintext">Version 3.4 exploits paired-end reads to explore possible contig merges within scaffolds (Consecutive contigs >= -z bases must overlap by -m bases or more). Version v3.4.1 allows a user to merge all contigs of a scaffold by padding predicted gaps with Ns (-n 1) and predicted but undetected overlaps with a single (n). Merged contigs are outputted in the .mergedcontigs file. The default behaviour (-n 0) is to NOT pad the gaps with Ns (v3.4 behaviour). In the v3.4.1, the .readposition file tracks read names instead of read sequences as the latter can be inferred from the start and end coordinates.</span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="plaintext"></span>
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161
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="plaintext">What's new in v3.3+ ?</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.3+ ?</span></span>
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163
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="plaintext"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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165
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown">Fixed a bug in PET routine. User can now track read position and individual base coverage for reads <span class="ge" style="font-style: italic;">*fully embedded*</span> within contigs, using the -c option.</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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166
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="plaintext"></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">What's new in v3.2.1+ ?</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.2.1+ ?</span></span>
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169
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="markdown"><span class="gh" style="color: #999;">-----------------------</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="plaintext"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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171
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown">This release runs ~30% faster and requires ~33% less RAM compared to 15-node prefix tree SSAKE v3.2.0.1 beta.</span>
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172
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown">Compared to the previous v3.2 release (11-node prefix tree), it will run at ca. double the speed, requiring ~20% more RAM.</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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173
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown"></span>
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174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="plaintext"></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="plaintext">What's new in v3.2+ ?</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.2+ ?</span></span>
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176
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="plaintext"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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178
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown">The -t option, first introduced in SSAKE 1.3, is back in this release. The option allows you to trim your contigs in 3', 1 base at a time until a maximum base trim value (-t) is reached. This option yields longer contigs, but increases assembly run time and, at high t values, might introduce contig misassemblies if your run parameters (i.e. -m, -o & -r) are not stringent enough. At -m 16 -o 3 -r 0.7, best results were obtained with -t 1. That's because it removes bases that cause premature breaks during the fragment assembly. If set, end-trimming kicks in only when all possibilities have been exhausted for a contig extension.</span>
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179
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown">This release also fixes a major bug that prevented SSAKE from exploring the entire read space for contig extensions seeded by the shorter reads.</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="markdown"></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="plaintext"></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="plaintext">What's new in v3.1+ ?</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.1+ ?</span></span>
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183
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="plaintext"></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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185
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="markdown">SSAKE now allows users to input a fasta file with DNA sequences for use as seeds to nucleate contig extension.</span>
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186
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown">This feature can be used to extend existing/known DNA sequences using millions of short reads.</span>
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187
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown">There's a new input format for paired-end reads, which allows reads of variable length to be considered (such as quality-trimmed reads)</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="plaintext"></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="plaintext">What's new in v3.0+ ?</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v3.0+ ?</span></span>
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191
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="plaintext"></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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193
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="markdown">SSAKE supports Illumina paired-end read data to build scaffolds. </span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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194
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="markdown"></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="plaintext"></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="plaintext">What's new in v2.0+ ?</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="markdown"><span class="gh" style="color: #999;">### What's new in v2.0+ ?</span></span>
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197
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="plaintext"></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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199
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="markdown">SSAKE can now handle error-rich data sets by looking through the overlapping k-mer space for consensus bases overhanging a seed sequence or contig.</span>
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200
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="markdown">SSAKE now runs on reads of various lengths. That means quality base trimming of individual sequences can be achieved (using TQS.py/TQSfastq.py supplied in ./tools directory).</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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201
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="markdown"></span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext"></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="plaintext">Implementation and requirements</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"><span class="gh" style="color: #999;">### Implementation and requirements</span></span>
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204
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------------------</span></span>
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="markdown"></span>
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206
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="markdown">SSAKE is implemented in PERL and runs on any OS where PERL is installed.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="222" style="width: 35px; color: rgba(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="206" style="width: 35px; color: rgba(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">@@ -222,18 +206,18 @@ PLEASE READ:</td>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="markdown">SSAKE might not be suited to work with 454-type reads. Simply because recurring base insertions/deletions errors, such as those commonly seen in homopolymeric regions, will not assemble well in the context of the SSAKE algorithm scheme. Sanger reads are ok, as long as reads are quality-trimmed.</span>
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext">Install</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>Install</span></span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="markdown"><span class="gh" style="color: #999;">-------</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="markdown">Download the tar ball, gunzip and extract the files on your system using:</span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext">gunzip ssake_v<span class="idiff left right">3-8-5</span>.tar.gz</span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="plaintext">tar -xvf ssake_v<span class="idiff left right">3-8-5</span>.tar</span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown">gunzip ssake_v<span class="idiff left right">4-0</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown">tar -xvf ssake_v<span class="idiff left right">4-0</span>.tar</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="markdown">Change the shebang line of SSAKE to point to the version of perl installed on your system and you're good to go.</span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="plaintext">Documentation</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>Documentation</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="markdown">Refer to the SSAKE.readme file on how to run SSAKE and the SSAKE web site for information about the software and its performance </span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="242" style="width: 35px; color: rgba(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="226" style="width: 35px; color: rgba(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">@@ -242,33 +226,35 @@ www.bcgsc.ca/bioinfo/software/ssake</td>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="markdown">Questions or comments? We would love to hear from you!</span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="plaintext">Citing SSAKE</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>Citing SSAKE</span></span>
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="markdown"><span class="gh" style="color: #999;">------------</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="markdown"></span>
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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="markdown">Thank you for using, developing and promoting this free software.</span>
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<td class="diff-line-num old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="markdown">If you use SSAKE for you research, please cite:</span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="markdown">Warren RL, Sutton GG, Jones SJM, Holt RA. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics. 23(4):500-501</span>
</pre>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="plaintext">Running SSAKE</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"><span class="gh" style="color: #999;">### Running SSAKE</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown">e.g. SSAKE -f paired.fa -m 20 -o 3 -r 0.7 -p 1 -c 1 -e 0.75 -l 5 -a 0.3 -z 50 -w 5 -g unpaired.fa </span>
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256
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="markdown"></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="plaintext">e.g. SSAKE -f paired.fa -m 17 -o 4 -r 0.7 -p 1 -c 1 -e 0.75 -k 2 -a 0.6 -z 50 -w 5 -g unpaired.fa </span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="plaintext">Usage: ./SSAKE [v3.8.5]</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown">Usage: ./SSAKE <span class="p">[</span><span class="nv" style="color: teal;">v4.0</span><span class="p">]</span></span>
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260
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="markdown">-f File containing all the <span class="p">[</span><span class="nv" style="color: teal;">paired (-p 1)</span><span class="p">]</span> reads (required)</span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="plaintext"> With -p 1:</span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="plaintext"> ! Target insert size must be indicated at the end of the header line (e.g. :200 for a 200bp insert)</span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="plaintext"> ! Paired reads must be separated by ":"</span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="plaintext"> >template_name:200</span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="plaintext"> ACGACACTATGCATAAGCAGACGAGCAGCGACGCAGCACG:GCGCACGACGCAGCACAGCAGCAGACGAC</span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="plaintext">-w Minimum depth of coverage allowed for contigs (e.g. -w 1 = process all reads [v3.7 behavior], required)</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"> With -p 1:</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"> ! Target insert size must be indicated at the end of the header line (e.g. :400 for a 400bp fragment/insert size)</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown"> ! Paired reads must be separated by ":"</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"><span class="gt" style="color: #a00;"> >header:400 (or >header_barcode:400)</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown"> ACGACACTATGCATAAGCAGACGAGCAGCGACGCAGCACG:GCGCACGACGCAGCACAGCAGCAGACGAC</span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown">-g Fasta file containing unpaired sequence reads (optional)</span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown">-w Minimum depth of coverage allowed for contigs (e.g. -w 1 = process all reads <span class="p">[</span><span class="nv" style="color: teal;">v3.7 behavior</span><span class="p">]</span>, required, recommended -w 5)</span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="markdown"> <span class="ge" style="font-style: italic;">*The assembly will stop when 50+ contigs with coverage < -w have been seen.*</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="markdown">-s Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)</span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="plaintext"><span class="idiff left right"> </span>-i Independent (de novo) assembly i.e Targets used to recruit reads for de novo assembly, not guide/seed reference-based assemblies (-i 1 = yes (default), 0 = no, optional)</span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext"><span class="idiff left right"> </span>-j Target sequence word size to hash (default -j 15)</span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="plaintext"><span class="idiff left right"> </span>-u Apply read space restriction to seeds while -s option in use (-u 1 = yes, default = no, optional)</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown"><span class="idiff left right"> </span>-i Independent (de novo) assembly i.e Targets used to recruit reads for de novo assembly, not guide/seed reference-based assemblies (-i 1 = yes (default), 0 = no, optional)</span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown"><span class="idiff left right"> </span>-j Target sequence word size to hash (default -j 15)</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown"><span class="idiff left right"> </span>-u Apply read space restriction to seeds while -s option in use (-u 1 = yes, default = no, optional)</span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="markdown">-m Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 20)</span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="markdown">-o Minimum number of reads needed to call a base during an extension (default -o 2)</span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="markdown">-r Minimum base ratio used to accept a overhang consensus base (default -r 0.7)</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">@@ -281,16 +267,19 @@ Usage: ./SSAKE [v3.8.5]</td>
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="markdown">-q Break tie when no consensus base at position, pick random base (-q 1 = yes, default = no, optional)</span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="markdown">-p Paired-end reads used? (-p 1 = yes, default = no, optional)</span>
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="markdown">-v Runs in verbose mode (-v 1 = yes, default = no, optional)</span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="plaintext">============ <span class="idiff left right">O</span>ptions below only considered with -p 1 ============</span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="markdown">============ <span class="idiff left right">scaffolding o</span>ptions below only considered with -p 1 ============</span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="markdown">-e Error (%) allowed on mean distance e.g. -e 0.75 == distance +/- 75% (default -e 0.75, optional)</span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="plaintext">-k Minimum number of links (read pairs) to compute scaffold (default -k 4, optional)</span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="plaintext">-a Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.5, optional)</span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="plaintext">-x Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -x 20, optional)</span>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext">-n N-pad gaps (-n 1 = yes, default = no 0, optional)</span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="plaintext">-g Fasta file containing unpaired sequence reads (optional)</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="markdown">-l Minimum number of links (read pairs) to compute scaffold (default -k 5, optional)</span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="markdown">-a Maximum link ratio between two best contig pairs <span class="ge" style="font-style: italic;">*higher values lead to least accurate scaffolding*</span> (default -a 0.3, optional)</span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="markdown">A BASIC PIPELINE TO HELP YOU PREPARE YOUR INPUT PAIRED READS EXISTS (./test/runSSAKE.sh)</span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="plaintext">Test data</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown">USAGE: ./runSSAKE.sh read1.fq read2.fq libraryFragmentLength basename</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="markdown"><span class="gh" style="color: #999;">### Test data</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="markdown"><span class="gh" style="color: #999;">---------</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="markdown">Go to the test folder, (cd test)</span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -305,7 +294,7 @@ The assembly above uses a single seed sequence located in (Herpesvirus_3.60kb.se</td>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="markdown">compare your results with Herpesvirus_3.60kb.reference.fa to see how successful the assembly was</span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="markdown">TEST DATA / SSAKE ASSEMBLIES</span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="markdown">A) Testing the distribution with very short reads:</span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="markdown">../SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -w 5 -c 1 </span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -328,15 +317,15 @@ C) Testing SSAKE on real (experimental) Illumina sequence data</td>
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="markdown">or </span>
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="markdown">./MiSeqCampylobacterAssembly.sh</span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="plaintext">(<span class="idiff left right">just the</span> assembly)</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="markdown">(<span class="idiff left right">read download,</span> assembly)</span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="markdown">3) Escherichia coli / 2014 Illumina MiSeq data</span>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="markdown">./MiSeqEcoliAssembly250XPE300.sh</span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="plaintext">(<span class="idiff left right">just the</span> assembly)</span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="markdown">(<span class="idiff left right">read download,</span> assembly)</span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="plaintext">This is illumina MiSeq base space data (one tenth of 2500-fold coverage run</span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="markdown">This is illumina MiSeq base space data (one tenth of 2500-fold coverage run<span class="idiff left right">)</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="markdown">sequence ~ 250X, 550bp fragments PE300</span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>compare your assembly to:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="346" style="width: 35px; color: rgba(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">@@ -346,7 +335,7 @@ coliMiSeq300m80.scaffolds.stats1</td>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="markdown">4) Fusobacterium nucleatum - CRC tumor isolate / Illumina HiSeq 2000 data</span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="markdown">./HiSeqFusobacteriumAssembly.sh</span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="plaintext">(<span class="idiff left right">just the</span> assembly)</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="markdown">(<span class="idiff left right">read download,</span> assembly)</span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="markdown">5) De Novo Targeted assembly of a TMPRSS2:ERG fusion using a prostate adenocarcinoma RNA-seq dataset</span>
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<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">@@ -354,7 +343,43 @@ coliMiSeq300m80.scaffolds.stats1</td>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="markdown">(read download,trimming,formatting,assembly)</span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="plaintext">How it works</span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="markdown">D) Testing SSAKE on LRsim linked-read data</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="markdown">1) C. elegans linked-read assembly</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="markdown">./CelegansLinkedReadsAssembly.sh</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown">(read download, assembly)</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="markdown">SSAKE v4.0 RUN TESTS (all tests provided in the test folder)</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="markdown">January 2018</span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="markdown">Contigs:</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="markdown">species|read type|n|n:500|L50|min|N80|N50|N20|E-size|max|sum|time (h:mm:ss)|RAM (GB)|file name</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="markdown">---|---|---|---|---|---|---|---|---|---|---|---|---|---|---</span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="markdown">Herpes virus|Illumina single-end|7|1|1|60000|60000|60000|60000|60000|60000|60000|0:00:22|0.2|HStestInstall_contigs.fa</span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="markdown">Ebola virus|Illumina paired-end|122|18|1|501|688|18917|18917|12139|18917|30101|0:01:22|0.4|ebola_contigs.fa</span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="markdown">F. nucleatum|HiSeq paired-end|697|560|131|501|2540|4641|8019|5631|19764|1937271|0:10:43|6.0|fusoCC53_contigs.fa</span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="markdown">C. showae|MiSeq paired-end|206|109|21|562|18061|32736|64004|40613|107028|2222124|0:06:58|3.5|CC57C_contigs.fa</span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="markdown">E. coli|MiSeq paired-end|101|97|12|687|80150|127399|210819|146845|318067|4606049|0:21:50|9.3|coliMiSeq300m80_contigs.fa</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="markdown">C. elegans|LRsim linked-read (paired) |5352|4949|613|502|19304|44626|90857|58011|305563|95.57e6|4:05:34|79.1|celegansLR_contigs.fa</span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="markdown">Scaffolds:</span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="markdown">species|read type|n|n:500|L50|min|N80|N50|N20|E-size|max|sum|name</span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="markdown">---|---|---|---|---|---|---|---|---|---|---|---|---</span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="markdown">F. nucleatum|HiSeq paired-end|638|524|120|501|2756|5067|9273|6141|19764|1943677|fusoCC53_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="markdown">C. showae|MiSeq paired-end|135|42|6|585|47914|128053|233500|159643|382374|2223249|Cshowae_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="markdown">E. coli|MiSeq paired-end|86|82|5|687|91172|204889|1193524|437907|1193524|4606049|coliMiSeq300m80_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="markdown">C. elegans|LRsim linked-read (paired)|4637|4309|491|502|22274|53866|112496|74063|357928|95.59e6|celegansLR_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="markdown">stats generated with abyss-fac</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="markdown">benchmark: Intel(R) Xeon(R) CPU E7-8867 v3 @ 2.50GHz 128CPU 2TB RAM CentOS7/ 1 thread per assembly</span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="markdown"><span class="gh" style="color: #999;">### How it works</span></span>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="markdown"><span class="gh" style="color: #999;">------------</span></span>
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="markdown"><span class="p">1.</span> Sequence Overlap</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">@@ -366,9 +391,11 @@ Once the search complete, a consensus sequence is derived from the hash table c,</td>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="markdown">The process of progressively cycling through longer to shorter 3'-most k-mer is repeated after every sequence extension until nothing else can be done on that side. Since only left-most searches are possible with a prefix tree, when all possibilities have been exhausted for the 3' extension, the complementary strand of the contiguous sequence generated is used to extend the contig on the 5' end. The DNA prefix tree is used to limit the search space by segregating sequence reads and their reverse-complemented counterparts by their first eleven 5' end bases. </span>
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392
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="markdown">There are three ways to control the stringency in SSAKE:</span>
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369
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="plaintext">1) Disallow read/contig extension if the coverage is too low (-o). Higher -o values lead to shorter contigs, but minimizes sequence misassemblies.</span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="plaintext">2) Adjust the minimum overlap -m allowed between the seed/contig and short sequence reads. Higher m values lead to more accurate contigs at the cost of decreased contiguity. </span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="plaintext">3) Set the minimum base ratio -r to higher values</span>
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="markdown">i) Disallow read/contig extension if the coverage is too low (-o). Higher -o values lead to shorter contigs, but minimizes sequence misassemblies.</span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="markdown">ii) Adjust the minimum overlap -m allowed between the seed/contig and short sequence reads. Higher m values lead to more accurate contigs at the cost of decreased contiguity. </span>
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="markdown">iii) Set the minimum base ratio -r to higher values</span>
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="markdown"><span class="p">2.</span> Building scaffolds with SSAKE</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="384" style="width: 35px; color: rgba(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="411" style="width: 35px; color: rgba(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">@@ -384,6 +411,7 @@ For each read pairs, putative contig pairs (pre-scaffolding stage) are tallied b</td>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="markdown">Please note that this stage accepts redundancy of contig pairs (i.e. a given contig may link to multiple contigs, and the number of links (spanning pairs) between any given contig pair is recorded, along with a mean putative gap or overlap(-)).</span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="markdown">Once pairing between contigs is complete, the scaffolds are built using contigs (-z or larger) as seeds. Every contig is used in turn until all have been incorporated into a scaffold.</span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="markdown">Consider the following contig pairs (AB, AC and rAD):</span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC417" class="line" lang="markdown"><span class="sb" style="color: #d14;"> A B</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="403" style="width: 35px; color: rgba(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="431" style="width: 35px; color: rgba(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">@@ -403,6 +431,7 @@ Consider the following contig pairs (AB, AC and rAD):</td>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="markdown"> -> <-</span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="markdown"> -> <-</span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="markdown"> -> <-</span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="markdown">Two parameters control scaffolding (-k and -a). The -k option specifies the minimum number of links (read pairs) a valid contig pair MUST have to be considered. The -a option specifies the maximum ratio between the best two contig pairs for a given seed/contig being extended. For example, contig A shares 4 links with B and 2 links with C, in this orientation. contig rA (reverse) also shares 3 links with D. When it's time to extend contig A (with the options -k and -a set to 2 and 0.7, respectively), both contig pairs AB and AC are considered. Since C (second-best) has 2 links and B (best) has 4 (2/4) = 0.5 below the maximum ratio of 0.7, A will be linked with B in the scaffold and C will be kept for another extension. If AC had 3 links the resulting ratio (0.75), above the user-defined maximum 0.7 would have caused the extension to terminate at A, with both B and C considered for a different scaffold. A maximum links ratio of 1 (not recommended) means that the best two candidate contig pairs have the same number of links -- SSAKE will accept the first one since both have a valid gap/overlap. When a scaffold extension is terminated on one side, the scaffold is extended on the "left", by looking for contig pairs that involve the reverse of the seed (in this example, rAD). With AB and AC having 4 and 2 links, respectively and rAD being the only pair on the left, the final scaffolds outputted by SSAKE would be:</span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="markdown"></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">@@ -417,7 +446,7 @@ Accurate scaffolding depends on many factors. Number and nature of repeats in y</td>
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<pre style="margin: 0;"> <span id="LC446" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="markdown">If the -s option is set and points to a valid fasta file, the DNA sequences comprised in that file will populate the hash table and be used exclusively as seeds to nucleate contig extensions (they will not be utilized to build the prefix tree). In that scheme, every unique seed will be used in turn to nucleate an extension, using short reads found in the tree (specified in -f). This feature might be useful if you already have characterized sequences & want to increase their length using short reads. That said, since the short reads are not used as seeds when -s is set, they will not co-assemble with one another WITHOUT a seed sequence file - unless you run SSAKE in targeted de novo assembly mode (see below). Also, to speed up the assembly, no imbedded reads (i.e. those aligning to the seed in their entirety) are considered. Only reads that contribute to extending a seed sequence are noted.</span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="plaintext">When -s is set, the <span class="idiff left right">.contigs</span> file lists all extended seeds, even if it's by a single base. The .singlets will ONLY list seeds that could not be extended. Unassembled microreads will NOT be outputted. </span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="markdown">When -s is set, the <span class="idiff left right">_contigs.fa</span> file lists all extended seeds, even if it's by a single base. The .singlets will ONLY list seeds that could not be extended. Unassembled microreads will NOT be outputted. </span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="markdown">Support for sequence target-independent de novo assemblies:</span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="markdown"></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">@@ -434,29 +463,51 @@ If more than one seed is supplied in the -s file and you're providing paired-end</td>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="plaintext">Input sequences</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>Input sequences</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="markdown">UNPAIRED:</span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="plaintext">DNA sequences can be in lower caps as well</span>
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<pre style="margin: 0;">-<span id="LC443" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="plaintext">>PX1CG<span class="idiff left right">_</span>29</span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="markdown">DNA sequences can be in lower caps as well<span class="idiff left right"> (NO UNDERSCORE _ CHARACTER ALLOWED)</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="markdown"><span class="gt" style="color: #a00;">>PX1CG29</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="markdown">TTAACACTTTCGGATATTTCTGATG</span>
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446
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="plaintext">>PX1CG<span class="idiff left right">_</span>35</span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="markdown"><span class="gt" style="color: #a00;">>PX1CG35</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="markdown">CTTTCGGATATTTCTGATGAGTCGA</span>
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<pre style="margin: 0;">-<span id="LC448" class="line" lang="plaintext">>PX1CG<span class="idiff left right">_</span>64</span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="markdown"><span class="gt" style="color: #a00;">>PX1CG64</span></span>
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="markdown">TTATCTTGATAAAGCAGGAATTACT</span>
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<pre style="margin: 0;"> <span id="LC479" class="line" lang="markdown">...</span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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481
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<pre style="margin: 0;"> <span id="LC481" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC482" class="line" lang="markdown">PAIRED:</span>
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<pre style="margin: 0;">-<span id="LC453" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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454
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484
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="markdown"><span class="gt" style="color: #a00;">>2-1-464-197:200</span></span>
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455
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="markdown">TGGCTCACCCCTGTAATCCCAGCACT:CTCCCAGGTTCAAGCGATTCTCCTGC</span>
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456
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486
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="markdown"><span class="gt" style="color: #a00;">>2-1-783-425:300</span></span>
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457
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="markdown">GTCTGAGGGTCCCAGGAACCAG:TGCCCCAGAGGTGGGAGCAGGGGA</span>
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458
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="markdown"><span class="gt" style="color: #a00;">>2-1-662-655:1000</span></span>
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459
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="markdown">TGAATCCCCACCAGGCGCCTTCGG:CACTTTATTATTAATGTACAAAAT</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="markdown">...</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="markdown">PAIRED, LINKED READ:</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="markdown"><span class="gt" style="color: #a00;">>2-1-464-197_ACGATGCATGCAGTAG:200</span></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="markdown">TGGCTCACCCCTGTAATCCCAGCACT:CTCCCAGGTTCAAGCGATTCTCCTGC</span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="markdown"><span class="gt" style="color: #a00;">>2-1-783-425_ACGATGCATGCAGTAG:300</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="markdown">GTCTGAGGGTCCCAGGAACCAG:TGCCCCAGAGGTGGGAGCAGGGGA</span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="markdown"><span class="gt" style="color: #a00;">>2-1-662-655_ATGCATGCATGCTAGC:1000</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="markdown">TGAATCCCCACCAGGCGCCTTCGG:CACTTTATTATTAATGTACAAAAT</span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="markdown">...</span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="markdown">-Note: For linked read, a barcode sequence of any length will do. In fact, any <span class="p">[</span><span class="nv" style="color: teal;">A-Za-z0-9</span><span class="p">]</span> characters after the underscore, before : or /<span class="se" style="color: #d14;">\ </span>will be used as barcode sequence to filter the reads. Note that when linked reads are not used, but regular reads are used instead, the original ssake behaviour will take precedence. Note that under NO circumstances should your read contain underscore characters (_) if your reads are NOT linked.</span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="markdown">Example input from the C. elegans test data available with the v4.0 distribution:</span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="markdown"><span class="gt" style="color: #a00;">>gi|453232919|ref|NCI003284.9|I11747444I11747218I1I0I0I0I0:0:0I0:0:0I98920/1_AAACCTGAGCTTTCAG/:350</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="markdown">CACATACGAGGGCGTTATTTGAAAAATTTAAAAATCAACATGTTCAAGCGTGCGAAGTGTCAAAATAAAAAAGAAAAAAAAAACGAAAAAAAAAACAGAAAAGGCTGATAAGAGGACGCGTCAAGTTA:ACTGCTCATTTGTCAATCAGCAAGGTACATGAAAACACAGAGCAGGAACCAAAATGCACACAATAAAACTCCCCGTACCCATTGTGTGGTACGCAGTACAAAATGACTGACAATAAGAAAGGGAGAGAGGGATTGAGGCGCCGAATACTTG</span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC512" class="line" lang="markdown">-Paired sequences must be concatenated together in one fasta-like entry, separated by ":". For example, TGGCTCACCCCTGTAATCCCAGCACT:CTCCCAGGTTCAAGCGATTCTCCTGC consists of two paired reads. Changes to the input was made to allow reads of variable length (e.g. quality-trimmed reads) to be considered by SSAKE. As of v3-6, the header line <span class="p">[</span><span class="nv" style="color: teal;">></span><span class="p">]</span> must have <span class="p">[</span><span class="nv" style="color: teal;">:insert_size</span><span class="p">]</span> at the very end (see above example)</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">@@ -472,31 +523,36 @@ General points:</td>
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<pre style="margin: 0;"> <span id="LC523" class="line" lang="markdown">-Spaces in fasta file are NOT permitted and will either not be considered or result in execution failure</span>
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<pre style="margin: 0;"> <span id="LC524" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="plaintext">Output files</span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>Output files</span></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="markdown"><span class="gh" style="color: #999;">------------</span></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="plaintext">.contigs :: fasta file; All sequence contigs</span>
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<pre style="margin: 0;">-<span id="LC479" class="line" lang="plaintext">.log :: text file; Logs execution time / errors / pairing stats (if -p is set to 1)</span>
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<pre style="margin: 0;">-<span id="LC480" class="line" lang="plaintext">.short :: text file; Lists sequence reads shorter than a set, acceptable, minimum</span>
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<pre style="margin: 0;">-<span id="LC481" class="line" lang="plaintext">.singlets :: fasta file; All unassembled sequence reads</span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="markdown">Output file (-p 0 and -p 1) | Description</span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="markdown">---|---</span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="markdown">_contigs.fa | fasta file; All sequence contigs</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="markdown">_scaffolds.fa |fasta file; All sequence scaffolds</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="markdown">.log | text file; Logs execution time / errors / pairing stats (if -p is set to 1)</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="markdown">_short.txt | text file; Lists sequence reads shorter than a set, acceptable, minimum</span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="markdown">_singlets.fa | fasta file; All unassembled sequence reads</span>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="plaintext"><span class="idiff left right">-p 1</span></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="plaintext"><span class="idiff left right">.pairing_distribution.csv :: comma-separated file; 1st column is the calculated distance for each pair (template) with reads that assembled logically within the same contig. 2nd column is the number of pairs at that distance</span></span>
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="plaintext"><span class="idiff left right">.pairing_issues :: text file; Lists all pairing issues encountered between contig pairs and illogical/out-of-bounds pairing</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="plaintext"><span class="idiff left right">.scaffolds :: comma-separated file; see below</span></span>
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="plaintext">.<span class="idiff left right">mergedcontigs :: fasta file; All merged/unmerged contigs >= -z bases within scaffolds are listed. The overlap sequence between contigs (>= -x bases) will be shown in lower case within the merged contig. Note that *perfect* sequence overlap has to occur between 2 predicted adjacent contigs of a scaffold in order to merge. It is possible that two contigs merge even though they are NOT predicted to do so (perhaps because insert size range supplied is off or mate pairs are misassembled). When two consecutive contigs do not physically overlap and the -n option is set to 1, then gaps will be padded with Ns of length corresponding to the predicted gap size m (refer to Understanding the .scaffolds csv file below) and predicted but undetected overlaps with a single (n).</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="markdown"><span class="idiff left right">Output file (-p 1) | Description</span></span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="markdown"><span class="idiff left right">---|---</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="markdown"><span class="idiff left right">_pairing-distribution.csv | comma-separated file; 1st column is the calculated distance for each pair (template) with reads that assembled logically within the same contig. 2nd column is the number of pairs at that distance</span></span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="markdown"><span class="idiff left right">_pairing-issues.txt | text file; Lists all pairing issues encountered between contig pairs and illogical/out-of-bounds pairing</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="markdown">.<span class="idiff left right">scaffolds | comma-separated file; see below</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="plaintext">-c 1 (WARNING: ASSOCIATED FILES CAN BECOME VERY LARGE!)</span>
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="plaintext">.readposition :: this is a text file listing all whole (fully embedded) reads, start and end coordinate onto the contig (in this order). For reads aligning on the minus strand, end coordinate is < start coordinate</span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="plaintext">.coverage.csv :: this is a comma-separated values file showing the base coverage at every position for any given contig > -z</span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="markdown">Output file (-c 1<span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>) | Description</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="markdown">---|---</span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="markdown">_readposition.txt | this is a text file listing all whole (fully embedded) reads, start and end coordinate onto the contig (in this order). For reads aligning on the minus strand, end coordinate is < start coordinate</span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="markdown">_coverage.csv | this is a comma-separated values file showing the base coverage at every position for any given contig > -z</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">*</span>WARNING: ASSOCIATED FILES CAN BECOME VERY LARGE!</span>
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="plaintext"><span class="idiff left right">Understanding the .contigs</span> fasta header</span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">#### Understanding the _contigs.fa</span> fasta header</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="markdown">e.g.</span>
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="markdown"><span class="gt" style="color: #a00;">>contig27|size52|read193|cov92.79</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="markdown">contig id# = 27</span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="markdown">size (G) = 52 nt</span>
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="markdown">number of reads (N) = 193</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">@@ -507,11 +563,12 @@ the coverage (C) is calculated using the total number (T) of consensus bases [su</td>
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<pre style="margin: 0;"> <span id="LC563" class="line" lang="markdown">C = T / G</span>
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<pre style="margin: 0;"> <span id="LC564" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="plaintext"><span class="idiff left right">Understanding the .scaffolds</span> csv file</span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">#### Understanding the .scaffolds layout</span> csv file</span></span>
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC512" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="markdown">e.g.</span>
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="markdown">scaffold1,7484,f127Z7068k12a0.58m42_f3090z62k7a0.14m76_f1473z354</span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="markdown"><span class="nt" style="color: navy;"></pre></span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="markdown">column 1: a unique scaffold identifier</span>
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<pre style="margin: 0;"> <span id="LC573" class="line" lang="markdown">column 2: the sum of all contig sizes that made it to the scaffold/supercontig</span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="markdown">column 3: a contig chain representing the layout:</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">@@ -525,19 +582,19 @@ Negative m values imply that there's a possible overlap between the contigs. Bu</td>
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="markdown">Use makeFastaFileFromScaffolds.pl included in this distribution to make a scaffold fasta file (ordered and oriented contig sequences) using the layout recipe (contig chain) shown above.</span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC528" class="line" lang="plaintext"><span class="idiff left right">Understanding the .</span>coverage.csv file</span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">#### Understanding the _</span>coverage.csv file</span></span>
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="markdown">e.g.</span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="markdown"><span class="gt" style="color: #a00;">>contig1|size60000|read74001|cov37.00</span></span>
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<pre style="margin: 0;"> <span id="LC590" class="line" lang="markdown">12,12,13,13,13,14,14,15,16,16,20,21,22,23,25,26,27,28,27 ...</span>
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="markdown">Each number represents the number of reads covering that base at that position.</span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="plaintext"><span class="idiff left right">Understanding the .readposition</span> file</span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">#### Understanding the _readposition.txt</span> file</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="markdown"><span class="gh" style="color: #999;">------------------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="markdown"><span class="nt" style="color: navy;"><pre></span></span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="markdown">e.g.</span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="markdown"><span class="gt" style="color: #a00;">>contig1|size60000|read74001|cov37.00</span></span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="markdown">READ_85952,3,32</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">@@ -552,23 +609,23 @@ READ_9721,15,44</td>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="markdown">READ_49141,16,45</span>
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="markdown">READ_43328,18,1</span>
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="markdown">READ_94449,18,1</span>
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<pre style="margin: 0;">-<span id="LC555" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="markdown">In this order: read name <span class="p">[</span><span class="nv" style="color: teal;">template th -p 1 :: name followed with 1 or 2, corresponds to the order in the sequence input (1:2)</span><span class="p">]</span>, start coordinate, end coordinate. end < start indicates read is on minus strand</span>
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="plaintext">SSAKE does not</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>SSAKE does not</span></span>
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------</span></span>
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC562" class="line" lang="plaintext"><span class="idiff left right">-</span>Take into consideration base quality scores. It is up to the user to process the sequence data before assembling with SSAKE.</span>
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<pre style="margin: 0;">-<span id="LC563" class="line" lang="plaintext"><span class="idiff left right"> Python scripts (TQS.py, TQSfastq.py, TQSexport.fq) are provided to help trim poor quality bases off Illumina sequences. </span> </span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="plaintext"><span class="idiff left right"> Refer to TQS.readme and TRIMMING_PAIRED_READS.README included in this distribution (in the ./tools subdirectory) for information on how to run those programs</span></span>
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<pre style="margin: 0;">-<span id="LC565" class="line" lang="plaintext"><span class="idiff left right">-Consider sequence read having any character other than A,C,G,T and will skip these reads entirely while reading the fasta file. </span></span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="markdown"><span class="p"><span class="idiff left">1.</span></span><span class="idiff right"> </span>Take into consideration base quality scores. It is up to the user to process the sequence data before assembling with SSAKE.</span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="markdown"><span class="p"><span class="idiff left">2.</span></span><span class="idiff right"> Consider sequence read having any character other than A,C,G,T and will skip these reads entirely while reading the fasta file.</span> </span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="markdown"><span class="idiff left right">Note: Python scripts (TQS.py, TQSfastq.py, TQSexport.fq) are provided to help trim poor quality bases off Illumina sequences. Refer to TQS.readme and TRIMMING_PAIRED_READS.README included in this distribution (in the ./tools subdirectory) for information on how to run those programs</span></span>
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC568" class="line" lang="plaintext">License</span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">### </span>License</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="markdown"><span class="gh" style="color: #999;">-------</span></span>
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC571" class="line" lang="plaintext">SSAKE Copyright (c) 2006-201<span class="idiff left right">6</span> Canada's Michael Smith Genome Science Centre. All rights reserved.</span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="markdown">SSAKE Copyright (c) 2006-201<span class="idiff left right">8</span> Canada's Michael Smith Genome Science Centre. All rights reserved.</span>
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<pre style="margin: 0;"> <span id="LC630" class="line" lang="markdown">This program is free software; you can redistribute it and/or</span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="markdown">modify it under the terms of the GNU General Public License</span>
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<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#99941e9e7cb4d8668499d7b495fec173b79dede0"><strong>test/CelegansLinkedReadsAssembly.sh</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span> </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline </span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Downloading trimmed/formatted data on <span class="nv" style="color: teal;">$d</span> ...</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell">rm <span class="nt" style="color: navy;">-rf</span> celegans_paired.fa</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell">wget ftp://ftp.bcgsc.ca/supplementary/SSAKE/celegans_paired.fa.gz</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell">gunzip celegans_paired.fa.gz</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Initiating SSAKE assembly</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> ../SSAKE <span class="nt" style="color: navy;">-f</span> celegans_paired.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-m</span> 20 <span class="nt" style="color: navy;">-w</span> 5 <span class="nt" style="color: navy;">-b</span> celegansLR</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from contigs</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">../tools/getStats.pl celegansLR_contigs.fa 500 <span class="o" style="font-weight: 600;">></span> celegansLR_contigs_stats.txt</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from scaffolds </span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">../tools/getStats.pl celegansLR_scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> celegansLR_scaffolds_stats.txt</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>assembly pipeline complete. Results are under celegansLR.</span></pre>
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<li id="c804969e079f8fb2205eca3e5403309119ac68c0">
<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#c804969e079f8fb2205eca3e5403309119ac68c0"><strong>test/Herpesvirus_3.60kb.reads.fa</strong></a>
The diff for this file was not included because it is too large.
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<li id="d6856a74a2823192c06c0ea5c349467fc7e5781e">
<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#d6856a74a2823192c06c0ea5c349467fc7e5781e"><strong>test/Herpesvirus_3.60kb.seed.fa</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">>seed<span class="idiff left right">_t</span>est</span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>seed<span class="idiff left right">T</span>est</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">TGACCAATACAAGAACATGTTCGATATATACTGGAATGAGTACGCCCCGGATATAGGGTTTTGTACATTTCCGGAGGAAGATGGCTGGATGTTAATACACCCAACCACGCAAAGTATGTTGTTTCGAAAAATCCTAGCCGGTGACTTTGGATATACCGATGGACAAGGCATATATAGCGCTGTACGGTCTACGGAAACTGTAATTCGCCAAGTTCAGGCAACCGTTTTGATGAACGCGTTGGATGCAACTCGGTATGAGGACCTAGCAGCAGATTGGGAACACCACATCCAACAATGTAACCTGCATGCCGGGGCTCTAGCGGAACGTTATGGGCTATGTGGAGAATCAGAAGCCGTACGGCTTGCACATCAGGTTTTTGAAACCTGGCGTCAAACATTACAGTCATCGTTACTTGAGTTTCTGCGTGGAATAACCGGTTGTCTCTATACCAGTGGTTTAAATGGAAGGGTCGGTTTTGCCAAATACGTGGACTGGATAGCCTGTGTAGGTATTGTGCCCGTTGTAAGAAAGGTACGATCAGAACAGAATGGAACCCCTGCACCATTAAATACGTATATGGGTCAAGCGGCAGAACTGTCCCAGATGTTAAAAGTTGCCGATGCAACGTTGGCCAGAGGAGCGGCGGTTGTCACAAGCCTAGTTGAGTGTATGCAAAATGTTGCTATTATGGATTATGATAGGACGCGTCTTTATTATAATTATAACCGAAGATTAATTATGGCAAAGGATGATGTAACGGGCATGAAGGGAGAGTGTTTGGTCGTGTGGCCGCCCGTTGTATGTGGGGAGGGTGTAGTATTTGACTCACCCTTACAGCGGCTTTCTGGGGAGGTGTTGGCCTGTTATGCATTACGTGAACATGCTCGCGTCTGCCAAGTTTTAAATACAGCCCCTTTGCGCGTGTTAATAGGTCGCCGGAATGAAGATGATAGATCTCACAGCACACGTGCGGTTGATCGTATAATGGGCGAGAACGATACAACACGGGCTGGATCGGCCGCGTCTAGACTTGTAAAGCTAATAGTTAACTTAAAAAACATGAGACATGTTGGAGATATTACCGAAACCGTACGTTCCTATCTAGAAGAAACGGGCAATCACATTCTGGAAGGAAGTGGATCGGTGGACACATCACAACCGGGGTTTGGCAAGGCCAACCAATCCTTTAACGGGGGGGCAATGTCCGGAACAACAAACGTTCAAAGTGCGTTTAAAACTTCGGTGGTTAACAGTATCAACGGCATGCTCGAGGGTTATGTGAAT</span></pre>
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<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#ffca57aa66e6a0dffe01e71bc059138782a383a7"><strong>test/HiSeqFusobacteriumAssembly.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span> </span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline on bacterial sequence data.<span class="idiff left right"> It will need ca.4GB RAM</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline on bacterial sequence data.</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="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</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="shell"><span class="nb" style="color: #0086b3;">echo </span>Downloading trimmed/formatted data <span class="k" style="font-weight: 600;">for </span>Fusobacterium nucleatum CC53 on <span class="nv" style="color: teal;">$d</span> ...</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(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="9" style="width: 35px; color: rgba(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">@@ -9,17 +9,12 @@ wget ftp://ftp.bcgsc.ca/supplementary/SSAKE/CC53_2million.fa</td>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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10
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Initiating SSAKE assembly ETA 10-20min depending on system...</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> ../SSAKE <span class="nt" style="color: navy;">-f</span> CC53_2million.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-m</span> 20 <span class="nt" style="color: navy;">-w</span> 5 <span class="nt" style="color: navy;">-b</span> fusoCC53<span class="idiff left right">-1</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> ../SSAKE <span class="nt" style="color: navy;">-f</span> CC53_2million.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-m</span> 20 <span class="nt" style="color: navy;">-w</span> 5 <span class="nt" style="color: navy;">-b</span> fusoCC53</span>
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13
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
</pre>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">nverting scaffold .csv into fasta file...</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">mputing stats from contigs</span></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">../tools/makeFastaFileFromScaffolds.pl fusoCC53-1.scaffolds</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">../tools/getStats.pl fusoCC53_contigs.fa 500 <span class="o" style="font-weight: 600;">></span> fusoCC53_contigs_stats.txt</span>
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<td class="diff-line-num new old_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">
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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="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from scaffolds </span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
17
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="19" 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="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from fusoCC53-1.contigs </span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
</pre>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">../tools/getStats.pl fusoCC53-1.contigs 500 <span class="o" style="font-weight: 600;">></span> fusoCC53-1.contigs.stats</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="22" 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="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from fusoCC53-1.scaffolds.fa</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">../tools/getStats.pl fusoCC53-1.scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> fusoCC53-1.scaffolds.stats</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>assembly pipeline complete. Results are under fusoCC53-1.</span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">../tools/getStats.pl fusoCC53_scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> fusoCC53_scaffolds_stats.txt</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>assembly pipeline complete. Results are under fusoCC53.</span></pre>
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<li id="5a72107eda85078f1e628667ed138e70e45b15e2">
<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#5a72107eda85078f1e628667ed138e70e45b15e2"><strong>test/MiSeqCampylobacterAssembly.sh</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span> </span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline on bacterial sequence data.<span class="idiff left right"> It will need ca.4GB RAM</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline on bacterial sequence data.</span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span> </span>
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5
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Downloading trimmed/formatted data <span class="k" style="font-weight: 600;">for </span>Campylobacter showae CC57C on <span class="nv" style="color: teal;">$d</span> ...</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(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="12" style="width: 35px; color: rgba(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">@@ -12,15 +12,11 @@ echo done. Initiating SSAKE assembly ETA 10-20min depending on system...</td>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> ../SSAKE <span class="nt" style="color: navy;">-f</span> CC57C_paired.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-g</span> CC57C_unpaired.fa <span class="nt" style="color: navy;">-m</span> 20 <span class="nt" style="color: navy;">-w</span> 5 <span class="nt" style="color: navy;">-b</span> CC57C</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">nverting scaffold .csv into fasta file...</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">mputing stats from contigs </span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell">../tools/<span class="idiff left right">makeFastaFileFromScaffolds.pl CC57C.scaffolds</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">../tools/<span class="idiff left">getStats.pl CC57C_contigs.fa 500 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> CC57C_contigs_stats.txt</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from <span class="idiff left right">CC57C.contigs </span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from <span class="idiff left right">scaffolds</span></span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">../tools/getStats.pl CC57C.contigs 500 <span class="o" style="font-weight: 600;">></span> CC57C.contigs.stats</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from CC57C.scaffolds.fa</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">------------------------------------------------------------------------------------</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">../tools/getStats.pl CC57C.scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> CC57C.scaffolds.stats</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">../tools/getStats.pl CC57C_scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> CC57C_scaffolds_stats.txt</span>
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26
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>assembly pipeline complete. Results are under CC57C.</span></pre>
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<li id="b03c5a3c850e023f0834b423398ebc5389d35400">
<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#b03c5a3c850e023f0834b423398ebc5389d35400"><strong>test/MiSeqCampylobacterAssemblyPIPELINE.sh</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span> </span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline on bacterial sequence data.<span class="idiff left right"> It will need ca.4GB RAM</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline on bacterial sequence data.</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="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span> </span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Downloading MiSeq data <span class="k" style="font-weight: 600;">for </span>Campylobacter showae CC57C on <span class="nv" style="color: teal;">$d</span> ...</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,15 +22,10 @@ echo done. Initiating SSAKE assembly ETA 10-20min depending on system...</td>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> ../SSAKE <span class="nt" style="color: navy;">-f</span> paired.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-g</span> unpaired.fa <span class="nt" style="color: navy;">-m</span> 20 <span class="nt" style="color: navy;">-w</span> 5 <span class="nt" style="color: navy;">-b</span> Cshowae</span>
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">nverting scaffold .csv into fasta file...</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">mputing stats from contigs </span></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell">../tools/makeFastaFileFromScaffolds.pl Cshowae.scaffolds</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">../tools/getStats.pl Cshowae_contigs.fa 500 <span class="o" style="font-weight: 600;">></span> Cshowae_contigs_stats.fa</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from scaffolds</span>
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28
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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29
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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from Cshowae.contigs </span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell">../tools/getStats.pl Cshowae.contigs 500 <span class="o" style="font-weight: 600;">></span> Cshowae.contigs.stats</span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from Cshowae.scaffolds.fa</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell">../tools/getStats.pl Cshowae.scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> Cshowae.scaffolds.stats</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell">../tools/getStats.pl Cshowae_scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> Cshowae_scaffolds_stats.txt</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>assembly pipeline complete. Results are under Cshowae.</span></pre>
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<br>
</li>
<li id="14067394c88a5c00f20cfec36a49e779ab061911">
<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#14067394c88a5c00f20cfec36a49e779ab061911"><strong>test/MiSeqEbolaAssemblyPIPELINE.sh</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(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">@@ -19,19 +19,14 @@ echo done. Formatting fasta input for SSAKE...</td>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell">../tools/makePairedOutput2UNEQUALfiles.pl SRR2019530_1.fastqc70q20e33.trimFIX.fa SRR2019530_2.fastqc70q20e33.trimFIX.fa 600</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Initiating SSAKE assembly<span class="idiff left right"> ETA 10-20min depending on system...</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Initiating SSAKE assembly<span class="idiff left right">.. </span></span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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24
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">time</span> ../SSAKE <span class="nt" style="color: navy;">-f</span> paired.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-g</span> unpaired.fa <span class="nt" style="color: navy;">-m</span> 20 <span class="nt" style="color: navy;">-w</span> 5 <span class="nt" style="color: navy;">-b</span> ebola</span>
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25
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">nverting scaffold .csv into fasta file...</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Co<span class="idiff left right">mputing stats from ebola_contigs.fa </span></span>
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27
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell">../tools/makeFastaFileFromScaffolds.pl ebola.scaffolds</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">../tools/getStats.pl ebola_contigs.fa 500 <span class="o" style="font-weight: 600;">></span> ebola_contigs_stats.txt</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from ebola_scaffolds.fa</span>
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29
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
</pre>
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30
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<td class="diff-line-num new_line old" data-linenumber="31" 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="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from ebola.contigs </span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell">../tools/getStats.pl ebola.contigs 500 <span class="o" style="font-weight: 600;">></span> ebola.contigs.stats</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from ebola.scaffolds.fa</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell">../tools/getStats.pl ebola.scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> ebola.scaffolds.stats</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell">../tools/getStats.pl ebola_scaffolds.fa 500 <span class="o" style="font-weight: 600;">></span> ebola_scaffolds_stats.txt</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>assembly pipeline complete. Results are under ebola.</span></pre>
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<li id="a84f0d42402c7712ae52503a83988613be924e06">
<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#a84f0d42402c7712ae52503a83988613be924e06"><strong>test/MiSeqEcoliAssembly250XPE300.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,6 @@ d=`date`</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span> </span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>Running SSAKE assembly pipeline on bacterial sequence data 250X E.coli</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="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span> </span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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6
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell">rm <span class="nt" style="color: navy;">-rf</span> ecoli_miseqTrimmed<span class="k" style="font-weight: 600;">*</span>fa</span>
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7
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell">wget ftp://ftp.bcgsc.ca/supplementary/SSAKE/ecoli_miseqTrimmed_paired.fa</span>
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8
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell">wget ftp://ftp.bcgsc.ca/supplementary/SSAKE/ecoli_miseqTrimmed_unpaired.fa</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">@@ -11,16 +10,12 @@ echo done. Initiating SSAKE assembly ETA 20-30min depending on system...</td>
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11
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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12
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell">/usr/bin/time <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-o</span> coliMiSeq300m80.time ../SSAKE <span class="nt" style="color: navy;">-f</span> ecoli_miseqTrimmed_paired.fa <span class="nt" style="color: navy;">-g</span> ecoli_miseqTrimmed_unpaired.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-m</span> 80 <span class="nt" style="color: navy;">-w</span> 100 <span class="nt" style="color: navy;">-b</span> coliMiSeq300m80</span>
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13
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Converting scaffold .csv into fasta file...</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell">../tools/makeFastaFileFromScaffolds.pl coliMiSeq300m80.scaffolds</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from Ecoli.contigs </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from contigs </span>
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19
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">../tools/getStats.pl coliMiSeq300m80<span class="idiff left">.contigs </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> coliMiSeq300m80.contigs.stats</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">../tools/getStats.pl coliMiSeq300m80<span class="idiff left">_contigs.fa </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> coliMiSeq300m80_contigs_stats.txt</span></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from <span class="idiff left right">Ecoli.scaffolds.fa</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span><span class="k" style="font-weight: 600;">done</span><span class="nb" style="color: #0086b3;">.</span> Computing stats from <span class="idiff left right">scaffolds</span></span>
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23
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell">../tools/getStats.pl coliMiSeq300m80<span class="idiff left">.scaffolds.fa 200 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> coliMiSeq300m80.scaffolds.200stats</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell">../tools/getStats.pl coliMiSeq300m80<span class="idiff left">.scaffolds.fa 500 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> coliMiSeq300m80.scaffolds.500stats</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">../tools/getStats.pl coliMiSeq300m80<span class="idiff left">_scaffolds.fa 200 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> coliMiSeq300m80_scaffolds_200bpstats.txt</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">../tools/getStats.pl coliMiSeq300m80<span class="idiff left">_scaffolds.fa 500 </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff right"> coliMiSeq300m80_scaffolds_500bpstats.txt</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo </span>assembly pipeline complete. Results are under coliMiSeq300m80.</span></pre>
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<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#d1969d87e396fe52d20be461548207ca94101d6e"><strong>test/README.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">January 201<span class="idiff left right">6</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">January 201<span class="idiff left right">8</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">------------</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">TEST DATA / SSAKE ASSEMBLIES</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">A) Testing the distribution with very short reads:</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">../SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -w 5 -c 1 </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">../SSAKE -f Herpesvirus_3.60kb.reads.fa -m 16 -o 2 -w 5 -c 1 <span class="idiff left right">-b HStestInstall </span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">B) Testing the targeted assembly using a seed/target sequence:</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">@@ -51,7 +51,7 @@ coliMiSeq300m80.scaffolds.stats1</td>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">./HiSeqFusobacteriumAssembly.sh</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">(<span class="idiff left right">just the</span> assembly)</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">(<span class="idiff left right">read download,</span> assembly)</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">5) De Novo Targeted assembly of a TMPRSS2:ERG fusion using a prostate adenocarcinoma RNA-seq dataset</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">@@ -59,3 +59,10 @@ coliMiSeq300m80.scaffolds.stats1</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">./runSSAKEtargeted.sh</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">(read download,trimming,formatting,assembly)</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">6) C. elegans linked-read assembly</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">./CelegansLinkedReadsAssembly.sh</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">(read download, assembly)</span></pre>
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<a href="https://salsa.debian.org/med-team/ssake/commit/83012ff7613f6d92edbe8e0a22c60595221d5f6c#bd0bfa40a3704cac54c450ad67c66e1937008247"><strong>test/assembly_metrics_tests.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">SSAKE v4.0</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">January 2018</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Contigs:</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">n n:500 L50 min N80 N50 N20 E-size max sum time (h:mm:ss) RAM (GB) name</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">206 109 21 562 18061 32736 64004 40613 107028 2222124 0:06:58 3.5 CC57C_contigs.fa</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">5352 4949 613 502 19304 44626 90857 58011 305563 95.57e6 4:05:34 79.1 celegansLR_contigs.fa</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">101 97 12 687 80150 127399 210819 146845 318067 4606049 0:21:50 9.3 coliMiSeq300m80_contigs.fa</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">206 109 21 562 18061 32736 64004 40613 107028 2222124 0:07:22 3.5 Cshowae_contigs.fa</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">122 18 1 501 688 18917 18917 12139 18917 30101 0:01:22 0.4 ebola_contigs.fa</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">697 560 131 501 2540 4641 8019 5631 19764 1937271 0:10:43 6.0 fusoCC53_contigs.fa</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">7 1 1 60000 60000 60000 60000 60000 60000 60000 0:00:22 0.2 HStestInstall_contigs.fa</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Scaffolds:</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">n n:500 L50 min N80 N50 N20 E-size max sum name</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">135 42 6 585 47914 128053 233500 159643 382374 2223249 CC57C_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">4637 4309 491 502 22274 53866 112496 74063 357928 95.59e6 celegansLR_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">86 82 5 687 91172 204889 1193524 437907 1193524 4606049 coliMiSeq300m80_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">135 42 6 585 47914 128053 233500 159643 382374 2223249 Cshowae_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">122 18 1 501 688 18917 18917 12139 18917 30101 ebola_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">638 524 120 501 2756 5067 9273 6141 19764 1943677 fusoCC53_scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">stats generated with abyss-fac</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">benchmark: Intel(R) Xeon(R) CPU E7-8867 v3 @ 2.50GHz 128CPU 2TB RAM CentOS7/ 1 thread per assembly</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell">../tools/runSSAKE.sh</span></pre>
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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">@@ -33,19 +33,14 @@ echo ---------------------------------------------------------------------------</td>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="shell">/usr/bin/time <span class="nt" style="color: navy;">-v</span> <span class="nt" style="color: navy;">-o</span> <span class="nv" style="color: teal;">$4</span>.time ../SSAKE <span class="nt" style="color: navy;">-f</span> paired.fa <span class="nt" style="color: navy;">-p</span> 1 <span class="nt" style="color: navy;">-g</span> unpaired.fa <span class="nt" style="color: navy;">-m</span> 20 <span class="nt" style="color: navy;">-w</span> 5 <span class="nt" style="color: navy;">-b</span> <span class="nv" style="color: teal;">$4</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$d</span> : Converting scaffold .csv into fasta file...</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="shell">../tools/makeFastaFileFromScaffolds.pl <span class="nv" style="color: teal;">$4</span>.scaffolds</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$d</span> : Computing stats </span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="shell">../tools/getStats.pl <span class="nv" style="color: teal;">$4</span><span class="idiff left">.contigs </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">$4</span></span><span class="idiff right">.contigs.stats</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">../tools/getStats.pl <span class="nv" style="color: teal;">$4<span class="idiff left">_contigs</span></span><span class="idiff">.fa </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">$4_contigs_stats</span></span><span class="idiff right">.txt</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$d</span> : Computing stats from <span class="nv" style="color: teal;">$4</span><span class="idiff left right">.</span>scaffolds.fa</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$d</span> : Computing stats from <span class="nv" style="color: teal;">$4<span class="idiff left right">_</span>scaffolds</span>.fa</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="shell">../tools/getStats.pl <span class="nv" style="color: teal;">$4</span><span class="idiff left">.scaffolds.fa </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">$4</span></span><span class="idiff right">.scaffolds.stats</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell">../tools/getStats.pl <span class="nv" style="color: teal;">$4<span class="idiff left">_scaffolds</span></span><span class="idiff">.fa </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">$4_scaffolds</span></span><span class="idiff right">.stats.txt</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="shell"><span class="nv" style="color: teal;">d</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>date<span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nt" style="color: navy;">-----------------------------------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$d</span> : assembly pipeline complete. Results are under <span class="nv" style="color: teal;">$4</span><span class="nb" style="color: #0086b3;">.</span></span></pre>
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