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<h3>

Andreas Tille pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/unicycler">Debian Med / unicycler</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323">6b867d2e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-09-06T06:32:06Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.4.7+dfsg</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#09900232f8b5007cc6515613f2702ebb76b1b928">

docs/unicycler-polish.md

</a>

</li>

<li class="file-stats">

<a href="#e744b908ee9ce1e4160b49b480376d1efdd7b25d">

test/test_misc.py

</a>

</li>

<li class="file-stats">

<a href="#824ffbbb89432ab2e50617c2178af52fcc3ad21f">

unicycler/blast_func.py

</a>

</li>

<li class="file-stats">

<a href="#4b4ac77faee247c87cc5735b624c92ee2e523a9d">

unicycler/misc.py

</a>

</li>

<li class="file-stats">

<a href="#4eb59695ae6bf60b4521cf1afc17ef535260a5db">

unicycler/pilon_func.py

</a>

</li>

<li class="file-stats">

<a href="#1f941b6b2d8d60232d459f825127d673bce10b87">

unicycler/spades_func.py

</a>

</li>

<li class="file-stats">

<a href="#59fca07fac6fd9e5a326c480accace22111a2286">

unicycler/unicycler.py

</a>

</li>

<li class="file-stats">

<a href="#cc119f2ea3a554e6f391a4bb23554ee16d8489ee">

unicycler/unicycler_polish.py

</a>

</li>

<li class="file-stats">

<a href="#4ca27ed8dd1770540001efbc5ee5a9cce34f7366">

unicycler/version.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -53,6 +53,7 @@ And read about how we use it to complete bacterial genomes here:</td>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

53

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="p">    *</span> <span class="p">[</span><span class="nv" style="color: teal;">Known contamination</span><span class="p">](</span><span class="sx" style="color: #d14;">#known-contamination</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(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="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="p">    *</span> <span class="p">[</span><span class="nv" style="color: teal;">Manual multiplicity</span><span class="p">](</span><span class="sx" style="color: #d14;">#manual-multiplicity</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(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="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="markdown"><span class="p">    *</span> <span class="p">[</span><span class="nv" style="color: teal;">Manual completion</span><span class="p">](</span><span class="sx" style="color: #d14;">#manual-completion</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="p">    *</span> <span class="p">[</span><span class="nv" style="color: teal;">Using an external long-read assembly</span><span class="p">](</span><span class="sx" style="color: #d14;">#using-an-external-long-read-assembly</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(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="LC57" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Other included tools</span><span class="p">](</span><span class="sx" style="color: #d14;">#other-included-tools</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(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="58" style="width: 35px; color: rgba(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="LC58" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Paper</span><span class="p">](</span><span class="sx" style="color: #d14;">#paper</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(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="59" style="width: 35px; color: rgba(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="LC59" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Acknowledgements</span><span class="p">](</span><span class="sx" style="color: #d14;">#acknowledgements</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="367" style="width: 35px; color: rgba(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="368" style="width: 35px; color: rgba(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">@@ -367,40 +368,42 @@ usage: unicycler [-h] [--help_all] [--version] [-1 SHORT1] [-2 SHORT2] [-s UNPAI</td>

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<td class="diff-line-num new_line" data-linenumber="368" style="width: 35px; color: rgba(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="LC368" class="line" lang="markdown"><span class="sb" style="color: #d14;">Unicycler: an assembly pipeline for bacterial genomes</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="369" style="width: 35px; color: rgba(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="370" style="width: 35px; color: rgba(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="LC370" class="line" lang="markdown"><span class="sb" style="color: #d14;">Help:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="370" 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="diff-line-num new_line old" data-linenumber="371" 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="LC370" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -h, --help                     <span class="idiff left right">      </span>Show this help message and exit</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="371" 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="diff-line-num new_line old" data-linenumber="371" 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="LC371" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --help_all                     <span class="idiff left right">      </span>Show a help message with all program options</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="372" 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="diff-line-num new_line old" data-linenumber="371" 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="LC372" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --version                      <span class="idiff left right">      </span>Show Unicycler's version number</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="373" style="width: 35px; color: rgba(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="LC371" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -h, --help                     Show this help message and exit</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

372

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<pre style="margin: 0;">+<span id="LC372" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --help_all                     Show a help message with all program options</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="373" style="width: 35px; color: rgba(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="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

373

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --version                      Show Unicycler's version number</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

373

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<td class="diff-line-num new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

374

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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="LC374" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

374

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<td class="diff-line-num new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

375

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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="LC375" class="line" lang="markdown"><span class="sb" style="color: #d14;">Input:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="375" 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">

375

</td>

<td class="diff-line-num new_line old" data-linenumber="376" 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="LC375" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -1 SHORT1, --short1 SHORT1           FASTQ file of first short reads in each pair (required)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="376" 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">

376

</td>

<td class="diff-line-num new_line old" data-linenumber="376" 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="LC376" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -2 SHORT2, --short2 SHORT2           FASTQ file of second short reads in each pair (required)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="377" 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">

377

</td>

<td class="diff-line-num new_line old" data-linenumber="376" 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="LC377" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -s UNPAIRED, --unpaired UNPAIRED     FASTQ file of unpaired short reads (optional)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="378" 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">

378

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<td class="diff-line-num new_line old" data-linenumber="376" 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="LC378" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -l LONG, --long LONG                 FASTQ or FASTA file of long reads (optional)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(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="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

376

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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="LC376" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -1 SHORT1, --short1 SHORT1     FASTQ file of first short reads in each pair (required)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(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="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

377

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -2 SHORT2, --short2 SHORT2     FASTQ file of second short reads in each pair (required)</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(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="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

378

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -s UNPAIRED, --unpaired UNPAIRED</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(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="379" style="width: 35px; color: rgba(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="LC379" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 FASTQ file of unpaired short reads (optional)</span></span>

</pre>

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</tr>

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<td class="diff-line-num new old_line" data-linenumber="379" style="width: 35px; color: rgba(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="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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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="LC380" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -l LONG, --long LONG           FASTQ or FASTA file of long reads (optional)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

379

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<td class="diff-line-num new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

381

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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="LC381" class="line" lang="markdown"></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

380

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<td class="diff-line-num new_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

382

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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="LC382" class="line" lang="markdown"><span class="sb" style="color: #d14;">Output:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="381" 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">

381

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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -o OUT, --out OUT                    Output directory (required)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="382" 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">

382

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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC382" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --verbosity VERBOSITY                Level of stdout and log file information (default: 1)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

383

</td>

<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                         0 = no stdout, 1 = basic progress indicators, 2 = extra info,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="384" 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">

384

</td>

<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                         3 = debugging info</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

385

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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_fasta_length MIN_FASTA_LENGTH  Exclude contigs from the FASTA file which are shorter than this length</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC386" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                       (default: 100)</span></span>

</pre>

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387

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<pre style="margin: 0;">-<span id="LC387" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --keep KEEP                          Level of file retention (default: 1)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC388" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                         0 = only keep final files: assembly (FASTA, GFA and log),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                         1 = also save graphs at main checkpoints,</span></span>

</pre>

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390

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<pre style="margin: 0;">-<span id="LC390" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                         2 = also keep SAM (enables fast rerun in different mode),</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                         3 = keep all temp files and save all graphs (for debugging)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC392" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --vcf                                Produce a VCF by mapping the short reads to the final assembly</span></span>

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                       (experimental, default: do not produce a vcf file)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC383" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -o OUT, --out OUT              Output directory (required)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC384" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --verbosity VERBOSITY          Level of stdout and log file information (default: 1)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC385" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   0 = no stdout, 1 = basic progress indicators, 2 = extra info,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC386" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   3 = debugging info</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC387" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_fasta_length MIN_FASTA_LENGTH</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC388" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 Exclude contigs from the FASTA file which are shorter than this</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC389" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 length (default: 100)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC390" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --keep KEEP                    Level of file retention (default: 1)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC391" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   0 = only keep final files: assembly (FASTA, GFA and log),</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   1 = also save graphs at main checkpoints,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   2 = also keep SAM (enables fast rerun in different mode),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC394" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   3 = keep all temp files and save all graphs (for debugging)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC395" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --vcf                          Produce a VCF by mapping the short reads to the final assembly</span></span>

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 (experimental, default: do not produce a vcf file)</span></span>

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="markdown"></span>

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<td class="diff-line-num new_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="markdown"><span class="sb" style="color: #d14;">Other:</span></span>

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -t THREADS, --threads THREADS  <span class="idiff left right">      </span>Number of threads used (default: 8)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --mode {conservative,normal,bold}<span class="idiff left right">    Bridging mode (default: normal)</span></span></span>

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">        conservative = smaller contigs, lowest misassembly rate</span></span></span>

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   <span class="idiff left right">      normal = moderate contig size and</span> misassembly rate</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   <span class="idiff left right">      bold = longest contigs, higher</span> misassembly rate</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC401" class="line" lang="markdown"><span class="sb" style="color: #d14;">  <span class="idiff left right">--linear_seqs LINEAR_SEQS            The expected number of linear (i.e. non-circular) sequences in th</span>e</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="markdown"><span class="sb" style="color: #d14;">  <span class="idiff left right">                                     underlying sequence (default: 0)</span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC403" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="markdown"><span class="sb" style="color: #d14;">  -t THREADS, --threads THREADS  Number of threads used (default: 8)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --mode {conservative,normal,bold}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">Bridging mode (default: normal)</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   <span class="idiff left right">conservative = smaller contigs, lowest</span> misassembly rate</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC403" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                   <span class="idiff left right">normal = moderate contig size and</span> misassembly rate</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="404" style="width: 35px; color: rgba(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="LC404" class="line" lang="markdown"><span class="sb" style="color: #d14;">  <span class="idiff left right">                                 bold = longest contigs, higher misassembly rat</span>e</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="markdown"><span class="sb" style="color: #d14;">  <span class="idiff left right">--linear_seqs LINEAR_SEQS      The expected number of linear (i.e. non-circular) sequences in</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC406" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 the underlying sequence (default: 0)</span></span>

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="markdown"><span class="p">```</span></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Advanced options</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">@@ -409,77 +412,96 @@ Run `unicycler --help_all` to see a complete list of the program's options. Thes</td>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="markdown"><span class="p">```</span></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="markdown"><span class="sb" style="color: #d14;">SPAdes assembly:</span></span>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the short-read SPAdes assembly at the beginning of the Unicycler pipeline.</span></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="sb" style="color: #d14;">  --spades_path SPADES_PATH           Path to the SPAdes executable (default: spades.py)</span></span>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_correct                        Skip SPAdes error correction step (default: conduct SPAdes error</span></span>

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      correction)</span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_kmer_frac MIN_KMER_FRAC       Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read</span></span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      length (default: 0.2)</span></span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --max_kmer_frac MAX_KMER_FRAC       Highest k-mer size for SPAdes assembly, expressed as a fraction of the read</span></span>

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      length (default: 0.95)</span></span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --kmer_count KMER_COUNT             Number of k-mer steps to use in SPAdes assembly (default: 10)</span></span>

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --depth_filter DEPTH_FILTER         Filter out contigs lower than this fraction of the chromosomal depth, if</span></span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      doing so does not result in graph dead ends (default: 0.25)</span></span>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the short-read SPAdes assembly at the beginning of the Unicycler</span></span>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="markdown"><span class="sb" style="color: #d14;">  pipeline.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC417" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --spades_path SPADES_PATH      Path to the SPAdes executable (default: spades.py)</span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_correct                   Skip SPAdes error correction step (default: conduct SPAdes error</span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 correction)</span></span>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_kmer_frac MIN_KMER_FRAC  Lowest k-mer size for SPAdes assembly, expressed as a fraction of</span></span>

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<pre style="margin: 0;">+<span id="LC422" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 the read length (default: 0.2)</span></span>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --max_kmer_frac MAX_KMER_FRAC  Highest k-mer size for SPAdes assembly, expressed as a fraction</span></span>

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<pre style="margin: 0;">+<span id="LC424" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 of the read length (default: 0.95)</span></span>

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<pre style="margin: 0;">+<span id="LC425" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --kmers KMERS                  Exact k-mers to use for SPAdes assembly, comma-separated</span></span>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 (example: 22,33,44, default: automatic)</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --kmer_count KMER_COUNT        Number of k-mer steps to use in SPAdes assembly (default: 10)</span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --depth_filter DEPTH_FILTER    Filter out contigs lower than this fraction of the chromosomal</span></span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 depth, if doing so does not result in graph dead ends (default:</span></span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 0.25)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --spades_tmp_dir SPADES_TMP_DIR</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 Specify SPAdes temporary directory using the SPAdes --tmp-dir</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 option (default: make a temporary directory in the output</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 directory)</span></span>

</pre>

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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"><span class="sb" style="color: #d14;">miniasm+Racon assembly:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the use of miniasm and Racon to produce long-read bridges.</span></span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_miniasm                        Skip miniasm+Racon bridging (default: use miniasm and Racon to produce</span></span>

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<pre style="margin: 0;">-<span id="LC429" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      long-read bridges)</span></span>

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --racon_path RACON_PATH             Path to the Racon executable (default: racon)</span></span>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_miniasm                   Skip miniasm+Racon bridging (default: use miniasm and Racon to</span></span>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 produce long-read bridges)</span></span>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --racon_path RACON_PATH        Path to the Racon executable (default: racon)</span></span>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --existing_long_read_assembly EXISTING_LONG_READ_ASSEMBLY</span></span>

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<pre style="margin: 0;">+<span id="LC443" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 A pre-prepared long read assembly for the sample in GFA format.</span></span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 If this option is used, Unicycler will skip the miniasm/Racon</span></span>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 steps and instead use the given assembly (default: perform long</span></span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 read assembly using miniasm/Racon)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="markdown"><span class="sb" style="color: #d14;">Assembly rotation:</span></span>

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<pre style="margin: 0;">-<span id="LC433" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the rotation of completed circular sequence near the end of the Unicycler pipeline.</span></span>

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<pre style="margin: 0;">-<span id="LC434" class="line" lang="markdown"></span>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_rotate                         Do not rotate completed replicons to start at a standard gene (default:</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      completed replicons are rotated)</span></span>

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<pre style="margin: 0;">-<span id="LC437" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --start_genes START_GENES           FASTA file of genes for start point of rotated replicons (default:</span></span>

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      start_genes.fasta)</span></span>

</pre>

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439

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<pre style="margin: 0;">-<span id="LC439" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --start_gene_id START_GENE_ID       The minimum required BLAST percent identity for a start gene search</span></span>

</pre>

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440

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<pre style="margin: 0;">-<span id="LC440" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      (default: 90.0)</span></span>

</pre>

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441

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --start_gene_cov START_GENE_COV     The minimum required BLAST percent coverage for a start gene search</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC442" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      (default: 95.0)</span></span>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the rotation of completed circular sequence near the end of the</span></span>

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="markdown"><span class="sb" style="color: #d14;">  Unicycler pipeline.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC451" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_rotate                    Do not rotate completed replicons to start at a standard gene</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC453" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 (default: completed replicons are rotated)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC454" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --start_genes START_GENES      FASTA file of genes for start point of rotated replicons</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 (default: start_genes.fasta)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC456" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --start_gene_id START_GENE_ID  The minimum required BLAST percent identity for a start gene</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 search (default: 90.0)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC458" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --start_gene_cov START_GENE_COV</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC459" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 The minimum required BLAST percent coverage for a start gene</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 search (default: 95.0)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --makeblastdb_path MAKEBLASTDB_PATH</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC444" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">     </span>Path to the makeblastdb executable (default: makeblastdb)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC445" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --tblastn_path TBLASTN_PATH    <span class="idiff left right">     </span>Path to the tblastn executable (default: tblastn)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="462" style="width: 35px; color: rgba(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="LC462" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 Path to the makeblastdb executable (default: makeblastdb)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="446" style="width: 35px; color: rgba(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="463" style="width: 35px; color: rgba(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="LC463" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --tblastn_path TBLASTN_PATH    Path to the tblastn executable (default: tblastn)</span></span>

</pre>

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446

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="447" style="width: 35px; color: rgba(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="465" style="width: 35px; color: rgba(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="LC465" class="line" lang="markdown"><span class="sb" style="color: #d14;">Pilon polishing:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="448" 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="diff-line-num new_line old" data-linenumber="466" 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="LC448" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the final assembly polish using Pilon at the end of the Unicycler pipeline.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="449" style="width: 35px; color: rgba(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="466" style="width: 35px; color: rgba(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="LC466" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the final assembly polish using Pilon at the end of the Unicycler</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="449" style="width: 35px; color: rgba(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="467" style="width: 35px; color: rgba(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="LC467" class="line" lang="markdown"><span class="sb" style="color: #d14;">  pipeline.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="468" style="width: 35px; color: rgba(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="LC468" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="450" 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="diff-line-num new_line old" data-linenumber="469" 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="LC450" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_pilon                          Do not use Pilon to polish the final assembly (default: Pilon is used)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="451" 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="diff-line-num new_line old" data-linenumber="469" 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="LC451" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --bowtie2_path BOWTIE2_PATH         Path to the bowtie2 executable (default: bowtie2)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="452" style="width: 35px; color: rgba(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="469" style="width: 35px; color: rgba(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="LC469" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_pilon                     Do not use Pilon to polish the final assembly (default: Pilon is</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="452" style="width: 35px; color: rgba(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="470" style="width: 35px; color: rgba(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="LC470" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 used)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="452" style="width: 35px; color: rgba(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="471" style="width: 35px; color: rgba(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="LC471" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --bowtie2_path BOWTIE2_PATH    Path to the bowtie2 executable (default: bowtie2)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="452" style="width: 35px; color: rgba(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="472" style="width: 35px; color: rgba(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="LC472" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --bowtie2_build_path BOWTIE2_BUILD_PATH</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="453" 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="diff-line-num new_line old" data-linenumber="473" 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="LC453" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      Path to the bowtie2_build executable (default: bowtie2-build)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="454" 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="diff-line-num new_line old" data-linenumber="473" 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="LC454" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --samtools_path SAMTOOLS_PATH       Path to the samtools executable (default: samtools)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="455" 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="diff-line-num new_line old" data-linenumber="473" 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="LC455" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --pilon_path PILON_PATH             Path to a Pilon executable or the Pilon Java archive file (default: pilon)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="456" 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">

456

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<td class="diff-line-num new_line old" data-linenumber="473" 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="LC456" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --java_path JAVA_PATH               Path to the java executable (default: java)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="457" 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="diff-line-num new_line old" data-linenumber="473" 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="LC457" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_polish_size MIN_POLISH_SIZE   Contigs shorter than this value (bp) will not be polished using Pilon</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="458" 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="LC458" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                      (default: 10000)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="473" style="width: 35px; color: rgba(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="LC473" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 Path to the bowtie2_build executable (default: bowtie2-build)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="459" style="width: 35px; color: rgba(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="474" style="width: 35px; color: rgba(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="LC474" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --samtools_path SAMTOOLS_PATH  Path to the samtools executable (default: samtools)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="475" style="width: 35px; color: rgba(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="LC475" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --pilon_path PILON_PATH        Path to a Pilon executable or the Pilon Java archive file</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="476" style="width: 35px; color: rgba(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="LC476" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 (default: pilon)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="477" style="width: 35px; color: rgba(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="LC477" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --java_path JAVA_PATH          Path to the java executable (default: java)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="478" style="width: 35px; color: rgba(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="LC478" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_polish_size MIN_POLISH_SIZE</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="479" style="width: 35px; color: rgba(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="LC479" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 Contigs shorter than this value (bp) will not be polished using</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="480" style="width: 35px; color: rgba(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="LC480" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 Pilon (default: 10000)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="481" style="width: 35px; color: rgba(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="LC481" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="460" style="width: 35px; color: rgba(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="482" style="width: 35px; color: rgba(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="LC482" class="line" lang="markdown"><span class="sb" style="color: #d14;">VCF:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="461" style="width: 35px; color: rgba(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="483" style="width: 35px; color: rgba(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="LC483" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the production of the VCF of the final assembly.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="484" style="width: 35px; color: rgba(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="LC484" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="463" 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="diff-line-num new_line old" data-linenumber="485" 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="LC463" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --bcftools_path BCFTOOLS_PATH  <span class="idiff left right">     </span>Path to the bcftools executable (default: bcftools)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="464" style="width: 35px; color: rgba(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="485" style="width: 35px; color: rgba(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="LC485" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --bcftools_path BCFTOOLS_PATH  Path to the bcftools executable (default: bcftools)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="464" style="width: 35px; color: rgba(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="486" style="width: 35px; color: rgba(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="LC486" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="465" style="width: 35px; color: rgba(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="487" style="width: 35px; color: rgba(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="LC487" class="line" lang="markdown"><span class="sb" style="color: #d14;">Graph cleaning:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="488" style="width: 35px; color: rgba(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="LC488" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the removal of small leftover sequences after bridging is complete.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="489" style="width: 35px; color: rgba(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="LC489" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="468" style="width: 35px; color: rgba(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="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_component_size MIN_COMPONENT_SIZE</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="469" 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="diff-line-num new_line old" data-linenumber="491" 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="LC469" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">     Graph components smaller than this size (bp) will be removed from the final</span></span></span>

</pre>

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470

</td>

<td class="diff-line-num new_line old" data-linenumber="491" 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="LC470" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">    </span> graph (default: 1000)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="471" style="width: 35px; color: rgba(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="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

491

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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="LC491" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">Graph components smaller than this size (bp) will be removed from</span></span></span>

</pre>

</td>

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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="471" style="width: 35px; color: rgba(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="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

492

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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="LC492" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">the final</span> graph (default: 1000)</span></span>

</pre>

</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="471" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

471

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<td class="diff-line-num new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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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="LC493" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_dead_end_size MIN_DEAD_END_SIZE</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="472" 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">

472

</td>

<td class="diff-line-num new_line old" data-linenumber="494" 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="LC472" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">     Graph dead ends smaller than this size (bp) will be removed from the final</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="473" 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">

473

</td>

<td class="diff-line-num new_line old" data-linenumber="494" 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="LC473" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">    </span> graph (default: 1000)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="474" style="width: 35px; color: rgba(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="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

494

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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="LC494" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">Graph dead ends smaller than this size (bp) will be removed from</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="474" style="width: 35px; color: rgba(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="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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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="LC495" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">the final</span> graph (default: 1000)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

474

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<td class="diff-line-num new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

496

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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="LC496" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

475

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<td class="diff-line-num new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

497

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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="LC497" class="line" lang="markdown"><span class="sb" style="color: #d14;">Long read alignment:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

476

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="markdown"><span class="sb" style="color: #d14;">  These options control the alignment of long reads to the assembly graph.</span></span>

</pre>

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<td class="diff-line-num 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">

477

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<td class="diff-line-num new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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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="LC499" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="478" 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">

478

</td>

<td class="diff-line-num new_line old" data-linenumber="500" 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="LC478" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --contamination CONTAMINATION  <span class="idiff left right">     </span>FASTA file of known contamination in long reads</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="479" 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">

479

</td>

<td class="diff-line-num new_line old" data-linenumber="500" 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="LC479" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --scores SCORES                <span class="idiff left right">     Comma-delimited string of alignment scores: match, mismatch, gap open</span>, gap</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="480" 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">

480

</td>

<td class="diff-line-num new_line old" data-linenumber="500" 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="LC480" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">    </span> extend (default: 3,-6,-5,-2)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="481" 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">

481

</td>

<td class="diff-line-num new_line old" data-linenumber="500" 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="LC481" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --low_score LOW_SCORE          <span class="idiff left right">     Score threshold - alignments below this are considered poor (default: set</span></span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="482" 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">

482

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<td class="diff-line-num new_line old" data-linenumber="500" 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="LC482" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">    </span> threshold automatically)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="483" style="width: 35px; color: rgba(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="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --contamination CONTAMINATION  FASTA file of known contamination in long reads</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="483" style="width: 35px; color: rgba(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="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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<pre style="margin: 0;">+<span id="LC501" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --scores SCORES                <span class="idiff left right">Comma-delimited string of alignment scores: match, mismatch</span>, gap</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="483" style="width: 35px; color: rgba(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="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">open, gap</span> extend (default: 3,-6,-5,-2)</span></span>

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --low_score LOW_SCORE          <span class="idiff left right">Score threshold - alignments below this are considered poor</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="markdown"><span class="sb" style="color: #d14;">                                 <span class="idiff left right">(default: set</span> threshold automatically)</span></span>

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="620" style="width: 35px; color: rgba(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="642" style="width: 35px; color: rgba(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">@@ -620,6 +642,12 @@ If you believe this has happened in your assembly, you can manually assign multi</td>

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="markdown">If Unicycler doesn't complete your bacterial genome assembly on its own, you may be able to complete it manually with a bit of bioinformatics detective work. There's no single, straight-forward procedure for doing so, but I've put together <span class="p">[</span><span class="nv" style="color: teal;">a few examples on the Unicycler wiki</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rrwick/Unicycler/wiki/Tips-for-finishing-genomes</span><span class="p">)</span> which may be helpful.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC645" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Using an external long-read assembly</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC646" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC647" class="line" lang="markdown">If you have a long-read assembly that you've prepared outside Unicycler and trust (e.g. with Canu), you can give it to Unicycler with <span class="sb" style="color: #d14;">`--existing_long_read_assembly`</span>. Unicycler will then skip its miniasm/Racon step and use this assembly instead.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="648" style="width: 35px; color: rgba(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="LC648" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="649" style="width: 35px; color: rgba(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="LC649" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC650" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="markdown"><span class="gh" style="color: #999;"># Other included tools</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="markdown"></span>

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<br>

</li>

<li id="09900232f8b5007cc6515613f2702ebb76b1b928">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#09900232f8b5007cc6515613f2702ebb76b1b928"><strong>docs/unicycler-polish.md</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,6 +85,7 @@ Generic long reads:</td>

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85

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"><span class="sb" style="color: #d14;">Polishing settings:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="sb" style="color: #d14;">  Various settings for polishing behaviour (defaults should work well in most cases)</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --no_fix_local                        do not fix local misassemblies (default: False)</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_insert MIN_INSERT               minimum valid short read insert size (default: auto)</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --max_insert MAX_INSERT               maximum valid short read insert size (default: auto)</span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"><span class="sb" style="color: #d14;">  --min_align_length MIN_ALIGN_LENGTH   Minimum long read alignment length (default: 1000)</span></span>

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<br>

</li>

<li id="e744b908ee9ce1e4160b49b480376d1efdd7b25d">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#e744b908ee9ce1e4160b49b480376d1efdd7b25d"><strong>test/test_misc.py</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">@@ -372,6 +372,13 @@ class TestMiscFunctions(unittest.TestCase):</td>

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python">        <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unicycler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">java_version_from_java_output</span><span class="p">(</span><span class="n" style="color: #333;">java_version_output</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_java_version_parsing_6</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python">        <span class="n" style="color: #333;">java_version_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'openjdk version "9-Ubuntu"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> \</span>

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python">                              <span class="s" style="color: #d14;">'OpenJDK Runtime Environment (build 9-Ubuntu+0-9b181-4)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> \</span>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python">                              <span class="s" style="color: #d14;">'OpenJDK 64-Bit Server VM (build 9-Ubuntu+0-9b181-4, mixed mode)'</span></span>

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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python">        <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unicycler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">java_version_from_java_output</span><span class="p">(</span><span class="n" style="color: #333;">java_version_output</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="s" style="color: #d14;">'9-Ubuntu'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_spades_version_parsing_1</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python">        <span class="n" style="color: #333;">spades_version_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'SPAdes v3.10.1'</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">        <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unicycler</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">misc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">spades_version_from_spades_output</span><span class="p">(</span><span class="n" style="color: #333;">spades_version_output</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="824ffbbb89432ab2e50617c2178af52fcc3ad21f">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#824ffbbb89432ab2e50617c2178af52fcc3ad21f"><strong>unicycler/blast_func.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" style="width: 35px; color: rgba(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="36" style="width: 35px; color: rgba(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">@@ -36,6 +36,7 @@ def find_start_gene(sequence, start_genes_fasta, identity_threshold, coverage_th</td>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(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="LC36" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># gene overlaps from the end to the start, we have to duplicate some of the replicon sequence</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># for the BLAST database.</span></span>

</pre>

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<td class="diff-line-num old_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">

38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">seq_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(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="39" style="width: 35px; color: rgba(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="LC39" class="line" lang="python">    <span class="n" style="color: #333;">start_genes_fasta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">start_genes_fasta</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">    <span class="n" style="color: #333;">queries</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">load_fasta</span><span class="p">(</span><span class="n" style="color: #333;">start_genes_fasta</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">queries</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">CannotFindStart</span></span>

</pre>

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<br>

</li>

<li id="4b4ac77faee247c87cc5735b624c92ee2e523a9d">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#4b4ac77faee247c87cc5735b624c92ee2e523a9d"><strong>unicycler/misc.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1070" style="width: 35px; color: rgba(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="1070" style="width: 35px; color: rgba(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">@@ -1070,19 +1070,29 @@ def java_path_and_version(java_path):</td>

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<td class="diff-line-num old_line" data-linenumber="1070" style="width: 35px; color: rgba(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="1070" style="width: 35px; color: rgba(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="LC1070" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1071" style="width: 35px; color: rgba(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="1071" style="width: 35px; color: rgba(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="LC1071" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># Make sure Java is 1.7+</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1072" style="width: 35px; color: rgba(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="1072" style="width: 35px; color: rgba(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="LC1072" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1073" 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="diff-line-num new_line old" data-linenumber="1073" 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="LC1073" class="line" lang="python">        <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1074" 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="diff-line-num new_line old" data-linenumber="1073" 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="LC1074" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1075" 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="diff-line-num new_line old" data-linenumber="1073" 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="LC1075" class="line" lang="python">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'too old'</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1076" 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="diff-line-num new_line old" data-linenumber="1073" 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="LC1076" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1077

</td>

<td class="diff-line-num new_line old" data-linenumber="1073" 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="LC1077" class="line" lang="python">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'good'</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1078" 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">

1078

</td>

<td class="diff-line-num new_line old" data-linenumber="1073" 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="LC1078" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># major_version == 1</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1079" 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">

1079

</td>

<td class="diff-line-num new_line old" data-linenumber="1073" 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="LC1079" class="line" lang="python">            <span class="n" style="color: #333;">minor_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="1080" 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">

1080

</td>

<td class="diff-line-num new_line old" data-linenumber="1073" 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="LC1080" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">minor_version</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1073" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1073

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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="LC1073" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'.'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">version</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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

</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="LC1074" class="line" lang="python">            <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1075" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1075

</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="LC1075" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1076" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1076

</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="LC1076" class="line" lang="python">                <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'too old'</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1077" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1077

</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="LC1077" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1078" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1078

</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="LC1078" class="line" lang="python">                <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'good'</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1079" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1079

</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="LC1079" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span>  <span class="c" style="color: #998; font-style: italic;"># major_version == 1</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1080" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1080

</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="LC1080" class="line" lang="python">                <span class="n" style="color: #333;">minor_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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

</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="LC1081" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">minor_version</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1082

</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="LC1082" class="line" lang="python">                    <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'too old'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1083

</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="LC1083" class="line" lang="python">                <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1084

</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="LC1084" class="line" lang="python">                    <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'good'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<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

</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="LC1085" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'-'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">version</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<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

</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="LC1086" class="line" lang="python">            <span class="c" style="color: #998; font-style: italic;"># E.g. '9-Ubuntu'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<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

</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="LC1087" class="line" lang="python">            <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1088

</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="LC1088" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">major_version</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1081" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1081

</td>

<td class="diff-line-num new_line" data-linenumber="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1089

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1089" class="line" lang="python">                <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'too old'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1082" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1082

</td>

<td class="diff-line-num new_line" data-linenumber="1090" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1090

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1090" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1083" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1083

</td>

<td class="diff-line-num new_line" data-linenumber="1091" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1091

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1091" class="line" lang="python">                <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'good'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1084" style="width: 35px; color: rgba(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="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

</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="LC1092" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="1084" style="width: 35px; color: rgba(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="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

</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="LC1093" class="line" lang="python">            <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'bad'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1084" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1084

</td>

<td class="diff-line-num new_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1094

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1094" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IndexError</span><span class="p">):</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="1085" 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">

1085

</td>

<td class="diff-line-num new_line old" data-linenumber="1095" 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="LC1085" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left">version</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">status</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">'?'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'too ol</span>d'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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">

</td>

<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

</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="LC1095" class="line" lang="python">        <span class="n" style="color: #333;"><span class="idiff left">status</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'ba</span>d'</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1086" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1086

</td>

<td class="diff-line-num new_line" data-linenumber="1096" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1096

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1096" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">found_java_path</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="n" style="color: #333;">status</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1087" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1087

</td>

<td class="diff-line-num new_line" data-linenumber="1097" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1097

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1097" class="line" lang="python"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1088

</td>

<td class="diff-line-num new_line" data-linenumber="1098" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1098

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC1098" class="line" lang="python"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="4eb59695ae6bf60b4521cf1afc17ef535260a5db">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#4eb59695ae6bf60b4521cf1afc17ef535260a5db"><strong>unicycler/pilon_func.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="336" style="width: 35px; color: rgba(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="336" style="width: 35px; color: rgba(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">@@ -336,7 +336,7 @@ def polish_with_pilon(graph, args, polish_dir, insert_size_1st, insert_size_99th</td>

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<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

336

</td>

<td class="diff-line-num new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

336

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC336" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">list_of_files</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

337

</td>

<td class="diff-line-num new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

337

</td>

<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC337" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="diff-line-num old_line" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

338

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<td class="diff-line-num new_line" data-linenumber="338" style="width: 35px; color: rgba(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="LC338" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;"><span class="idiff left right">FileNotFoundError</span></span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="340" style="width: 35px; color: rgba(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="339" style="width: 35px; color: rgba(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="LC339" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">FileNotFoundError</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">OSError</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="342" style="width: 35px; color: rgba(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="LC342" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">total_count</span></span>

</pre>

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<br>

</li>

<li id="1f941b6b2d8d60232d459f825127d673bce10b87">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#1f941b6b2d8d60232d459f825127d673bce10b87"><strong>unicycler/spades_func.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +73,7 @@ def get_best_spades_graph(short1, short2, short_unpaired, out_dir, read_depth_fi</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">        <span class="n" style="color: #333;">kmer_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmers</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(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="LC74" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">        <span class="n" style="color: #333;">kmer_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_kmer_range</span><span class="p">(</span><span class="n" style="color: #333;">short1</span><span class="p">,</span> <span class="n" style="color: #333;">short2</span><span class="p">,</span> <span class="n" style="color: #333;">short_unpaired</span><span class="p">,</span> <span class="n" style="color: #333;">spades_dir</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_count</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python">                                    <span class="n" style="color: #333;">min_k_frac</span><span class="p">,</span> <span class="n" style="color: #333;">max_k_frac</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(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="LC76" class="line" lang="python">                                    <span class="n" style="color: #333;">min_k_frac</span><span class="p">,</span> <span class="n" style="color: #333;">max_k_frac</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">spades_path</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">    <span class="n" style="color: #333;">assem_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">spades_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'assembly'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(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="78" style="width: 35px; color: rgba(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="LC78" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" style="width: 35px; color: rgba(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="79" style="width: 35px; color: rgba(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="LC79" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log_section_header</span><span class="p">(</span><span class="s" style="color: #d14;">'SPAdes assemblies'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="427" style="width: 35px; color: rgba(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="427" style="width: 35px; color: rgba(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">@@ -427,8 +427,27 @@ def spades_assembly(read_files, out_dir, kmers, threads, spades_path, spades_tmp</td>

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<td class="diff-line-num old_line" data-linenumber="427" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

427

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<td class="diff-line-num new_line" data-linenumber="427" style="width: 35px; color: rgba(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="LC427" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">graph_files</span><span class="p">,</span> <span class="n" style="color: #333;">insert_size_mean</span><span class="p">,</span> <span class="n" style="color: #333;">insert_size_deviation</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="428" style="width: 35px; color: rgba(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="428" style="width: 35px; color: rgba(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="LC428" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_max_spades_kmer</span><span class="p">(</span><span class="n" style="color: #333;">spades_path</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"><span class="s" style="color: #d14;">    SPAdes usually has a maximum k-mer size of 127, but this can be changed when compiling SPAdes,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"><span class="s" style="color: #d14;">    so this function checks the help text to see what it is.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC434" class="line" lang="python"><span class="s" style="color: #d14;">    https://github.com/ablab/spades/issues/40</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC435" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC437" class="line" lang="python">        <span class="n" style="color: #333;">process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="n" style="color: #333;">spades_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'--help'</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC438" class="line" lang="python">                                   <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python">        <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">err</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">process</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python">        <span class="n" style="color: #333;">all_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">err</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">decode</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python">        <span class="n" style="color: #333;">all_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python">        <span class="n" style="color: #333;">all_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">' '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">all_output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">())</span></span>

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<td class="diff-line-num new new_line" data-linenumber="443" style="width: 35px; color: rgba(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="LC443" class="line" lang="python">        <span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">all_output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'must be odd and less than '</span><span class="p">)[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</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>

</pre>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">max_kmer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">127</span></span>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_kmer_range</span><span class="p">(</span><span class="n" style="color: #333;">reads_1_filename</span><span class="p">,</span> <span class="n" style="color: #333;">reads_2_filename</span><span class="p">,</span> <span class="n" style="color: #333;">unpaired_reads_filename</span><span class="p">,</span> <span class="n" style="color: #333;">spades_dir</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python">                   <span class="n" style="color: #333;">kmer_count</span><span class="p">,</span> <span class="n" style="color: #333;">min_kmer_frac</span><span class="p">,</span> <span class="n" style="color: #333;">max_kmer_frac</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python">                   <span class="n" style="color: #333;">kmer_count</span><span class="p">,</span> <span class="n" style="color: #333;">min_kmer_frac</span><span class="p">,</span> <span class="n" style="color: #333;">max_kmer_frac</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">spades_path</span></span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"><span class="s" style="color: #d14;">    Uses the read lengths to determine the k-mer range to be used in the SPAdes assembly.</span></span>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"><span class="s" style="color: #d14;">    """</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">@@ -453,6 +472,11 @@ def get_kmer_range(reads_1_filename, reads_2_filename, unpaired_reads_filename,</td>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python">                <span class="k" style="font-weight: 600;">pass</span></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python">    <span class="n" style="color: #333;">max_spades_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_max_spades_kmer</span><span class="p">(</span><span class="n" style="color: #333;">spades_path</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'SPAdes maximum k-mer: {}'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format</span><span class="p">(</span><span class="n" style="color: #333;">max_spades_kmer</span><span class="p">))</span></span>

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<td class="diff-line-num new new_line" data-linenumber="477" style="width: 35px; color: rgba(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="LC477" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_spades_kmer</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">127</span><span class="p">:</span></span>

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<td class="diff-line-num new new_line" data-linenumber="478" style="width: 35px; color: rgba(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="LC478" class="line" lang="python">        <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'    (unusual value, probably indicates custom SPAdes compilation)'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># If the code got here, then the k-mer range doesn't already exist and we'll create one by</span></span>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># examining the read lengths.</span></span>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python">    <span class="n" style="color: #333;">read_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_read_lengths</span><span class="p">(</span><span class="n" style="color: #333;">reads_1_filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">get_read_lengths</span><span class="p">(</span><span class="n" style="color: #333;">reads_2_filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</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">@@ -460,18 +484,25 @@ def get_kmer_range(reads_1_filename, reads_2_filename, unpaired_reads_filename,</td>

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python">    <span class="n" style="color: #333;">read_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">read_lengths</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python">    <span class="n" style="color: #333;">median_read_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_lengths</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read_lengths</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="mi" style="color: #099;">1</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python">    <span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">round_to_nearest_odd</span><span class="p">(</span><span class="n" style="color: #333;">max_kmer_frac</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">median_read_length</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC463" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;"><span class="idiff left right">127</span></span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python">        <span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;"><span class="idiff left right">127</span></span></span>

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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;"><span class="idiff left right">max_spades_kmer</span></span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC488" class="line" lang="python">        <span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">max_spades_kmer</span></span></span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python">    <span class="n" style="color: #333;">starting_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">round_to_nearest_odd</span><span class="p">(</span><span class="n" style="color: #333;">min_kmer_frac</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">max_kmer_frac</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">starting_kmer</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">11</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python">        <span class="n" style="color: #333;">starting_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">11</span></span>

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># Create the k-mer range from a non-linear function that spaces out the early k-mers more and</span></span>

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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python">    <span class="c" style="color: #998; font-style: italic;"># makes the later k-mers (which are most likely to be the good, used ones) closer together.</span></span>

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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python">    <span class="n" style="color: #333;">kmer_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<td class="diff-line-num new_line old" data-linenumber="493" 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="LC472" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">kmer_count</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">kmer_count</span><span class="p">)]:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="473" 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">

473

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<td class="diff-line-num new_line old" data-linenumber="493" 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="LC473" class="line" lang="python">        <span class="n" style="color: #333;">kmer_range</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">starting_kmer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">starting_kmer</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="474" 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">

474

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<td class="diff-line-num new_line old" data-linenumber="493" 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="LC474" class="line" lang="python">    <span class="n" style="color: #333;">kmer_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">round_to_nearest_odd</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kmer_range</span><span class="p">])))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

493

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kmer_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

494

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python">        <span class="n" style="color: #333;">kmer_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">max_kmer</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">kmer_count</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

496

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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python">        <span class="n" style="color: #333;">kmer_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">starting_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">max_kmer</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

497

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python">    <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="475" style="width: 35px; color: rgba(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="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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<pre style="margin: 0;">+<span id="LC498" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># Create the k-mer range from a non-linear function that spaces out the early k-mers more</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

499

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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># and makes the later k-mers (which are most likely to be the good, used ones) closer</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

500

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python">        <span class="c" style="color: #998; font-style: italic;"># together.</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

501

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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="LC501" class="line" lang="python">        <span class="n" style="color: #333;">kmer_range</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="475" style="width: 35px; color: rgba(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="502" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

502

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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">kmer_count</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">kmer_count</span><span class="p">)]:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="503" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

503

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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python">            <span class="n" style="color: #333;">kmer_range</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">max_kmer</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">starting_kmer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">starting_kmer</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

504

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python">        <span class="n" style="color: #333;">kmer_range</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">([</span><span class="n" style="color: #333;">round_to_nearest_odd</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kmer_range</span><span class="p">])))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="475" style="width: 35px; color: rgba(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="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

505

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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="LC505" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

475

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<td class="diff-line-num new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python">    <span class="n" style="color: #333;">kmer_range_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">', '</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">kmer_range</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="476" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

476

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<td class="diff-line-num new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

507

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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="LC507" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num 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">

477

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<td class="diff-line-num new_line" data-linenumber="508" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

508

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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="LC508" class="line" lang="python">    <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="s" style="color: #d14;">'Median read length: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">median_read_length</span><span class="p">))</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="59fca07fac6fd9e5a326c480accace22111a2286">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#59fca07fac6fd9e5a326c480accace22111a2286"><strong>unicycler/unicycler.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="493" style="width: 35px; color: rgba(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="493" style="width: 35px; color: rgba(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">@@ -493,6 +493,9 @@ def get_arguments():</td>

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<td class="diff-line-num old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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<td class="diff-line-num new_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">threads</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 old_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

494

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<td class="diff-line-num new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

494

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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="LC494" class="line" lang="python">        <span class="n" style="color: #333;">quit_with_error</span><span class="p">(</span><span class="s" style="color: #d14;">'--threads must be at least 1'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<td class="diff-line-num new_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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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="LC495" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="496" style="width: 35px; color: rgba(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="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

496

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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="LC496" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_count</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="496" style="width: 35px; color: rgba(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="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

497

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python">        <span class="n" style="color: #333;">quit_with_error</span><span class="p">(</span><span class="s" style="color: #d14;">'--kmer_count must be at least 1'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="496" style="width: 35px; color: rgba(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="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

498

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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="LC498" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

496

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<td class="diff-line-num new_line" data-linenumber="499" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

499

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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="LC499" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmers</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

497

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<td class="diff-line-num new_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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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="LC500" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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">

498

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<td class="diff-line-num new_line" data-linenumber="501" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

501

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="cc119f2ea3a554e6f391a4bb23554ee16d8489ee">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#cc119f2ea3a554e6f391a4bb23554ee16d8489ee"><strong>unicycler/unicycler_polish.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,6 +106,8 @@ def get_arguments():</td>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">    <span class="n" style="color: #333;">settings_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Polishing settings'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">                                               <span class="s" style="color: #d14;">'Various settings for polishing behaviour '</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">                                               <span class="s" style="color: #d14;">'(defaults should work well in most cases)'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python">    <span class="n" style="color: #333;">settings_group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--no_fix_local'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>

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<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(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="LC110" class="line" lang="python">                                <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'do not fix local misassemblies'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python">    <span class="n" style="color: #333;">settings_group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--min_insert'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">                                <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'minimum valid short read insert size (default: auto)'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python">    <span class="n" style="color: #333;">settings_group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--max_insert'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="410" style="width: 35px; color: rgba(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="412" style="width: 35px; color: rgba(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">@@ -410,6 +412,11 @@ def pilon_small_changes(fasta, round_num, args, all_ale_scores):</td>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pilon_large_changes</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">round_num</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">all_ale_scores</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">no_fix_local</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="416" style="width: 35px; color: rgba(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="LC416" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">verbosity</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="417" style="width: 35px; color: rgba(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="LC417" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'Not fixing local misassemblies'</span><span class="p">,</span> <span class="n" style="color: #333;">flush</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="418" style="width: 35px; color: rgba(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="LC418" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">round_num</span><span class="p">,</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="419" style="width: 35px; color: rgba(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="LC419" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="420" style="width: 35px; color: rgba(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="LC420" class="line" lang="python">    <span class="n" style="color: #333;">current</span><span class="p">,</span> <span class="n" style="color: #333;">round_num</span><span class="p">,</span> <span class="n" style="color: #333;">applied_variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ale_assessed_changes</span><span class="p">(</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span> <span class="n" style="color: #333;">round_num</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python">                                                               <span class="n" style="color: #333;">all_ale_scores</span><span class="p">,</span> <span class="s" style="color: #d14;">'local'</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python">                                                               <span class="s" style="color: #d14;">'Pilon polish, large variants, '</span></span>

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<li id="4ca27ed8dd1770540001efbc5ee5a9cce34f7366">

<a href="https://salsa.debian.org/med-team/unicycler/commit/6b867d2eeaddc1460170007da8c4972083a47323#4ca27ed8dd1770540001efbc5ee5a9cce34f7366"><strong>unicycler/version.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,4 +13,4 @@ details. You should have received a copy of the GNU General Public License along</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">not, see <http://www.gnu.org/licenses/>.</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.4.<span class="idiff left right">6</span>'</span></span></pre>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'0.4.<span class="idiff left right">7</span>'</span></span></pre>

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