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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/porechop">Debian Med / porechop</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/porechop/commit/9904cd8bf255135b069354758622ae612466aa0b">9904cd8b</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2018-10-23T11:53:12Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.2.4+dfsg</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#ed6e4c64fbfbb74aca7c1f7ae77cea47abb8c6f3">
porechop/adapters.py
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<li class="file-stats">
<a href="#bcc6990bda499ad6312bebe6fa27eddcd005e148">
porechop/nanopore_read.py
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<li class="file-stats">
<a href="#b3c5c58de7161317c864b8c5319db46fb841057a">
porechop/porechop.py
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<li class="file-stats">
<a href="#aea35a4ca593a300f3e36b82cee91a18d2a09955">
porechop/version.py
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/porechop/commit/9904cd8bf255135b069354758622ae612466aa0b#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,6 +5,13 @@ Porechop is a tool for finding and removing adapters from [Oxford Nanopore](http</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">Porechop also supports demultiplexing of Nanopore reads that were barcoded with the <span class="p">[</span><span class="nv" style="color: teal;">Native Barcoding Kit</span><span class="p">](</span><span class="sx" style="color: #d14;">https://store.nanoporetech.com/native-barcoding-kit-1d.html</span><span class="p">)</span>, <span class="p">[</span><span class="nv" style="color: teal;">PCR Barcoding Kit</span><span class="p">](</span><span class="sx" style="color: #d14;">https://store.nanoporetech.com/pcr-barcoding-kit-96.html</span><span class="p">)</span> or <span class="p">[</span><span class="nv" style="color: teal;">Rapid Barcoding Kit</span><span class="p">](</span><span class="sx" style="color: #d14;">https://store.nanoporetech.com/rapid-barcoding-sequencing-kit.html</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Oct 2018 update: Porechop is officially unsupported</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">While I'm happy Porechop has so many users, it has always been a bit klugey and a pain to maintain. I don't have the time to give it the attention it deserves, so I'm going to now officially declare Porechop as abandonware (though the unanswered <span class="p">[</span><span class="nv" style="color: teal;">issues</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rrwick/Porechop/issues</span><span class="p">)</span> and <span class="p">[</span><span class="nv" style="color: teal;">pull requests</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rrwick/Porechop/pulls</span><span class="p">)</span> reveal that it already has been for some time). I've added a <span class="p">[</span><span class="nv" style="color: teal;">known issues</span><span class="p">](</span><span class="sx" style="color: #d14;">#known-issues</span><span class="p">)</span> section to the README to outline what I think is wrong with Porechop and how a reimplementation should look. I may someday (no promises though :stuck_out_tongue:) try to rewrite it from a blank canvas to address its faults.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"><span class="gh" style="color: #999;"># Table of contents</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,6 +31,7 @@ Porechop also supports demultiplexing of Nanopore reads that were barcoded with</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: teal;">Verbose output</span><span class="p">](</span><span class="sx" style="color: #d14;">#verbose-output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Known adapters</span><span class="p">](</span><span class="sx" style="color: #d14;">#known-adapters</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Full usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#full-usage</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">Known issues</span><span class="p">](</span><span class="sx" style="color: #d14;">#known-issues</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" 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>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: teal;">License</span><span class="p">](</span><span class="sx" style="color: #d14;">#license</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,9 +99,6 @@ __Demultiplex barcoded reads:__<br></td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__Demultiplex barcoded reads, straight from Albacore output directory:__</span><span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"><span class="sb" style="color: #d14;">`porechop -i albacore_dir -b output_dir`</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__Demultiplex barcoded reads without trimming (appropriate if Nanopolish will be used):__</span><span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown"><span class="sb" style="color: #d14;">`porechop -i input_reads.fastq.gz -b output_dir --untrimmed`</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__Also works with FASTA:__</span><span class="nt" style="color: navy;"><br></span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"><span class="sb" style="color: #d14;">`porechop -i input_reads.fasta -o output_reads.fasta`</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,11 +148,9 @@ TGTTGTTGTTGTTATTGTTGTTATTGTTGTTGTATTGTTGTTATTGTTGTTGTTGTACATTGTTATTGTTGTATTGTTGT</td>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="markdown">If you run Porechop with <span class="sb" style="color: #d14;">`--discard_middle`</span>, the reads with internal adapters will be thrown out instead of split.</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="markdown">This approach might make sense if you are trimming reads from a barcoded run, as chimeric reads may combine sequences from different bins. For example, consider this read:</span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"><span class="sb" style="color: #d14;">BC01_rev - SEQUENCE_1 - SQK-NSK007_Y_Top - BC02_rev - SEQUENCE_2</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="markdown">SEQUENCE_1 belongs in the barcode 1 bin and SEQUENCE_2 belongs in the barcode 2 bin, so while we could split the read, we would end up with contamination from another bin. Throwing the read out with <span class="sb" style="color: #d14;">`--discard_middle`</span> might be the better option.</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown">If you plan on using your reads with <span class="p">[</span><span class="nv" style="color: teal;">Nanopolish</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/jts/nanopolish</span><span class="p">)</span>, then the <span class="sb" style="color: #d14;">`--discard_middle`</span> option is required. This is because Nanopolish first runs <span class="p">[</span><span class="nv" style="color: teal;">`nanopolish index`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/jts/nanopolish#data-preprocessing</span><span class="p">)</span> to find a one-to-one association between FASTQ reads and fast5 files. If you ran Porechop _without_ <span class="sb" style="color: #d14;">`--discard_middle`</span>, then you could end up with multiple separate FASTQ reads which are from a single fast5, and this is incompatible with Nanopolish.</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown">This option is also recommended if you are trimming reads from a demultiplexed barcoded sequencing run. This is because chimeric reads may contain two sequences from two separate barcodes, so throwing them out is the safer option to reduce cross-barcode contamination.</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Barcode demultiplexing</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">@@ -189,10 +192,10 @@ Alternately, you can run Porechop with `-b` which specifies a directory for barc</td>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown">If Porechop is run without <span class="sb" style="color: #d14;">`-o`</span> or <span class="sb" style="color: #d14;">`-b`</span>, then it will output the trimmed reads to stdout and print its progress info to stderr. The output format of the reads will be FASTA/FASTQ based on the input reads, or else can be specified using <span class="sb" style="color: #d14;">`--format`</span>.</span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`--verbosity`</span> option will change the <span class="idiff left right">outpu</span>t of progress info:</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`--verbosity`</span> option will change the <span class="idiff left right">amoun</span>t of progress info:</span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`--verbosity 0`</span> gives no progress output.</span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`--verbosity 1`</span> (<span class="idiff left right">the default) gives summary info about end adapter trimming and shows all instances of</span> middle adapter splitting.</span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`--verbosity 2`</span> shows <span class="idiff left right">sequences and is described below</span>.</span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`--verbosity 1`</span> (<span class="idiff left right">default) gives summary info about end adapter trimming and</span> middle adapter splitting.</span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`--verbosity 2`</span> shows <span class="idiff left right">the actual trimmed/split sequences for each read (described more below)</span>.</span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown"><span class="p">*</span> <span class="sb" style="color: #d14;">`--verbosity 3`</span> shows tons of data (mainly for debugging).</span>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="233" style="width: 35px; color: rgba(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="236" style="width: 35px; color: rgba(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">@@ -233,103 +236,143 @@ If you want to add your own adapter sequences to Porechop, you can do so by edit</td>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="markdown"><span class="gh" style="color: #999;"># Full usage</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="markdown"><span class="sb" style="color: #d14;">usage: porechop <span class="idiff left right">[-h] </span>-i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [-t THREADS] [-<span class="idiff left right">-version] [-</span>b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD]</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"><span class="sb" style="color: #d14;">usage: porechop -i INPUT [-o OUTPUT] [--format {auto,fasta,fastq,fasta.gz,fastq.gz}] [-v VERBOSITY]</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [-t THREADS] [-b BARCODE_DIR] [--barcode_threshold BARCODE_THRESHOLD]</span></span>
</pre>
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238
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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--barcode_diff BARCODE_DIFF] [--require_two_barcodes] [--untrimmed]</span></span>
</pre>
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239
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<td class="diff-line-num new_line old" data-linenumber="242" style="width: 35px; color: rgba(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="LC239" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--adapter_threshold ADAPTER_THRESHOLD] [--check_reads CHECK_READS]</span></span>
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240
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<td class="diff-line-num new_line old" data-linenumber="242" style="width: 35px; color: rgba(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="LC240" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--scoring_scheme SCORING_SCHEME] [--end_size END_SIZE] [--min_trim_size MIN_TRIM_SIZE]</span></span>
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241
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<td class="diff-line-num new_line old" data-linenumber="242" style="width: 35px; color: rgba(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="LC241" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--extra_end_trim EXTRA_END_TRIM] [--end_threshold END_THRESHOLD] [--discard_middle]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--discard_unassigned] [--adapter_threshold ADAPTER_THRESHOLD]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--check_reads CHECK_READS] [--scoring_scheme SCORING_SCHEME] [--end_size END_SIZE]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--min_trim_size MIN_TRIM_SIZE] [--extra_end_trim EXTRA_END_TRIM]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--end_threshold END_THRESHOLD] [--no_split] [--discard_middle]</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
242
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<td class="diff-line-num new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--middle_threshold MIDDLE_THRESHOLD]</span></span>
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<td class="diff-line-num old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
243
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247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE]</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
244
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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE]</span></span>
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245
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--min_split_read_size MIN_SPLIT_READ_SIZE]</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="markdown"></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="markdown"><span class="sb" style="color: #d14;">Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and splitting</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="markdown"><span class="sb" style="color: #d14;">reads with internal adapters</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"><span class="sb" style="color: #d14;"> [--min_split_read_size MIN_SPLIT_READ_SIZE] [-h] [--version]</span></span>
</pre>
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249
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="markdown"></span>
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250
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">optional arguments:</span></span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right"> -h, --help show this help message and exit</span></span></span>
</pre>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">Porechop: a tool for finding adapters in Oxford Nanopore reads, trimming them from the ends and</span></span></span>
</pre>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">splitting reads with internal adapters</span></span></span>
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252
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253
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="markdown"></span>
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253
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="markdown"><span class="sb" style="color: #d14;">Main options:</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -i INPUT, --input INPUT <span class="idiff left right"> FASTA/FASTQ of input reads or a directory which will be recursively</span></span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span> searched for FASTQ files (required)</span></span>
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o OUTPUT, --output OUTPUT <span class="idiff left right"> </span>Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span>reads will be printed to stdout)</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -i INPUT, --input INPUT <span class="idiff left right">FASTA/FASTQ of input reads or a directory which will be</span></span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right">recursively</span> searched for FASTQ files (required)</span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -o OUTPUT, --output OUTPUT Filename for FASTA or FASTQ of trimmed reads (if not set, trimmed</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="sb" style="color: #d14;"> reads will be printed to stdout)</span></span>
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258
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --format {auto,fasta,fastq,fasta.gz,fastq.gz}</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Output format for the reads - if auto, the format will be chosen based</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="markdown"><span class="sb" style="color: #d14;"> on the output filename or the input read format (default: auto)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Output format for the reads - if auto, the format will be chosen</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="markdown"><span class="sb" style="color: #d14;"> based on the output filename or the input read format (default:</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="markdown"><span class="sb" style="color: #d14;"> auto)</span></span>
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261
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -v VERBOSITY, --verbosity VERBOSITY</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Level of progress information: 0 = none, 1 = some, 2 = lots, 3 = full</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="markdown"><span class="sb" style="color: #d14;"> - output will go to stdout if reads are saved to a file and stderr if</span></span>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="markdown"><span class="sb" style="color: #d14;"> reads are printed to stdout (default: 1)</span></span>
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -t THREADS, --threads THREADS Number of threads to use for adapter alignment (default: 8)</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --version show program's version number and exit</span></span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Level of progress information: 0 = none, 1 = some, 2 = lots, 3 =</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="markdown"><span class="sb" style="color: #d14;"> full - output will go to stdout if reads are saved to a file and</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="markdown"><span class="sb" style="color: #d14;"> stderr if reads are printed to stdout (default: 1)</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -t THREADS, --threads THREADS Number of threads to use for adapter alignment (default: 8)</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="markdown"></span>
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268
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="markdown"><span class="sb" style="color: #d14;">Barcode binning settings:</span></span>
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269
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Control the binning of reads based on barcodes (i.e. barcode demultiplexing)</span></span>
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270
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="markdown"></span>
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271
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -b BARCODE_DIR, --barcode_dir BARCODE_DIR</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span>Reads will be binned based on their barcode and saved to separate</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span>files in this directory (incompatible with --output)</span></span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Reads will be binned based on their barcode and saved to separate</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="markdown"><span class="sb" style="color: #d14;"> files in this directory (incompatible with --output)</span></span>
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274
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --barcode_threshold BARCODE_THRESHOLD</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="markdown"><span class="sb" style="color: #d14;"> A read must have at least this percent identity to a barcode to be</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="markdown"><span class="sb" style="color: #d14;"> binned (default: 75.0)</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="markdown"><span class="sb" style="color: #d14;"> second-best barcode identity is less than this value, it will not be</span></span>
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279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="markdown"><span class="sb" style="color: #d14;"> put in a barcode bin (to exclude cases which are too close to call)</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="markdown"><span class="sb" style="color: #d14;"> (default: 5.0)</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --require_two_barcodes Reads will only be put in barcode bins if they have a strong match for</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="markdown"><span class="sb" style="color: #d14;"> the barcode on both their start and end (default: a read can be binned</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="markdown"><span class="sb" style="color: #d14;"> with a match at its start or end)</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --untrimmed Bin reads but do not trim the ends (appropriate if reads are to be</span></span>
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285
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="markdown"><span class="sb" style="color: #d14;"> used with Nanopolish) (default: False)</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="markdown"><span class="sb" style="color: #d14;"> A read must have at least this percent identity to a barcode to be</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown"><span class="sb" style="color: #d14;"> binned (default: 75.0)</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --barcode_diff BARCODE_DIFF If the difference between a read's best barcode identity and its</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="markdown"><span class="sb" style="color: #d14;"> second-best barcode identity is less than this value, it will not</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown"><span class="sb" style="color: #d14;"> be put in a barcode bin (to exclude cases which are too close to</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="markdown"><span class="sb" style="color: #d14;"> call) (default: 5.0)</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --require_two_barcodes Reads will only be put in barcode bins if they have a strong match</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="markdown"><span class="sb" style="color: #d14;"> for the barcode on both their start and end (default: a read can</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="markdown"><span class="sb" style="color: #d14;"> be binned with a match at its start or end)</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --untrimmed Bin reads but do not trim them (default: trim the reads)</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --discard_unassigned Discard unassigned reads (instead of creating a "none" bin)</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="markdown"><span class="sb" style="color: #d14;"> (default: False)</span></span>
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286
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="markdown"></span>
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287
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="markdown"><span class="sb" style="color: #d14;">Adapter search settings:</span></span>
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288
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Control how the program determines which adapter sets are present</span></span>
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="markdown"></span>
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290
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292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --adapter_threshold ADAPTER_THRESHOLD</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="markdown"><span class="sb" style="color: #d14;"> An adapter set has to have at least this percent identity to be</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="markdown"><span class="sb" style="color: #d14;"> labelled as present and trimmed off (0 to 100) (default: 90.0)</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --check_reads CHECK_READS This many reads will be aligned to all possible adapters to determine</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="markdown"><span class="sb" style="color: #d14;"> which adapter sets are present (default: 10000)</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --scoring_scheme SCORING_SCHEME Comma-delimited string of alignment scores: match, mismatch, gap open,</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="markdown"><span class="sb" style="color: #d14;"> gap extend (default: 3,-6,-5,-2)</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="markdown"><span class="sb" style="color: #d14;"> An adapter set has to have at least this percent identity to be</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="markdown"><span class="sb" style="color: #d14;"> labelled as present and trimmed off (0 to 100) (default: 90.0)</span></span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --check_reads CHECK_READS This many reads will be aligned to all possible adapters to</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="markdown"><span class="sb" style="color: #d14;"> determine which adapter sets are present (default: 10000)</span></span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --scoring_scheme SCORING_SCHEME</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Comma-delimited string of alignment scores: match, mismatch, gap</span></span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="markdown"><span class="sb" style="color: #d14;"> open, gap extend (default: 3,-6,-5,-2)</span></span>
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297
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300
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="markdown"></span>
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298
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301
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="markdown"><span class="sb" style="color: #d14;">End adapter settings:</span></span>
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299
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Control the trimming of adapters from read ends</span></span>
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300
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303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="markdown"></span>
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301
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --end_size END_SIZE The number of base pairs at each end of the read which will be</span></span>
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302
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="markdown"><span class="sb" style="color: #d14;"> searched for adapter sequences (default: 150)</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4)</span></span>
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304
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --extra_end_trim EXTRA_END_TRIM This many additional bases will be removed next to adapters found at</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="markdown"><span class="sb" style="color: #d14;"> the ends of reads (default: 2)</span></span>
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306
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent identity</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="markdown"><span class="sb" style="color: #d14;"> to be removed (0 to 100) (default: 75.0)</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --end_size END_SIZE The number of base pairs at each end of the read which will be</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="markdown"><span class="sb" style="color: #d14;"> searched for adapter sequences (default: 150)</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --min_trim_size MIN_TRIM_SIZE Adapter alignments smaller than this will be ignored (default: 4)</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --extra_end_trim EXTRA_END_TRIM</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="markdown"><span class="sb" style="color: #d14;"> This many additional bases will be removed next to adapters found</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="markdown"><span class="sb" style="color: #d14;"> at the ends of reads (default: 2)</span></span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --end_threshold END_THRESHOLD Adapters at the ends of reads must have at least this percent</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="markdown"><span class="sb" style="color: #d14;"> identity to be removed (0 to 100) (default: 75.0)</span></span>
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308
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="markdown"></span>
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309
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313
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="markdown"><span class="sb" style="color: #d14;">Middle adapter settings:</span></span>
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310
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Control the splitting of read from middle adapters</span></span>
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --no_split Skip splitting reads based on middle adapters (default: split reads</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="markdown"><span class="sb" style="color: #d14;"> when an adapter is found in the middle)</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --discard_middle Reads with middle adapters will be discarded (default: reads with</span></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="markdown"><span class="sb" style="color: #d14;"> middle adapters are split) (this option is on by default when</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="markdown"><span class="sb" style="color: #d14;"> outputting reads into barcode bins)</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --no_split Skip splitting reads based on middle adapters (default: split</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="markdown"><span class="sb" style="color: #d14;"> reads when an adapter is found in the middle)</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --discard_middle Reads with middle adapters will be discarded (default: reads with</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="markdown"><span class="sb" style="color: #d14;"> middle adapters are split) (required for reads to be used with</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Nanopolish, this option is on by default when outputting reads</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown"><span class="sb" style="color: #d14;"> into barcode bins)</span></span>
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --middle_threshold MIDDLE_THRESHOLD</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span>Adapters in the middle of reads must have at least this percent</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span>identity to be found (0 to 100) (default: 85.0)</span></span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Adapters in the middle of reads must have at least this percent</span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="markdown"><span class="sb" style="color: #d14;"> identity to be found (0 to 100) (default: 85.0)</span></span>
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320
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --extra_middle_trim_good_side EXTRA_MIDDLE_TRIM_GOOD_SIDE</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> This many additional bases will be removed next to middle adapters on</span></span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span> their "good" side (default: 10)</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right">This many additional bases will be removed next to middle adapters</span></span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right">on</span> their "good" side (default: 10)</span></span>
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323
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --extra_middle_trim_bad_side EXTRA_MIDDLE_TRIM_BAD_SIDE</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> This many additional bases will be removed next to middle adapters on</span></span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right"> </span> their "bad" side (default: 100)</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right">This many additional bases will be removed next to middle adapters</span></span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="markdown"><span class="sb" style="color: #d14;"> <span class="idiff left right">on</span> their "bad" side (default: 100)</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --min_split_read_size MIN_SPLIT_READ_SIZE</span></span>
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Post-split read pieces smaller than this many base pairs will not be</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="markdown"><span class="sb" style="color: #d14;"> outputted (default: 1000)</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="markdown"><span class="sb" style="color: #d14;"> Post-split read pieces smaller than this many base pairs will not</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="markdown"><span class="sb" style="color: #d14;"> be outputted (default: 1000)</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="markdown"><span class="sb" style="color: #d14;">Help:</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="markdown"><span class="sb" style="color: #d14;"> -h, --help Show this help message and exit</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="markdown"><span class="sb" style="color: #d14;"> --version Show program's version number and exit</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="markdown"><span class="p">```</span></span>
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339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="markdown"></span>
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="markdown"></span>
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341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="markdown"><span class="gh" style="color: #999;"># Known issues</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Adapter search</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="markdown">Porechop tries to automatically determine which adapters are present by looking at the reads, but this approach has a few issues:</span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="markdown"><span class="p">*</span> As the number of kits/barcodes has grown, adapter-search part of the Porechop's pipeline has become increasingly slow.</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="markdown"><span class="p">*</span> Porechop only does the adapter search on a subset of reads, which means there can be problems with non-randomly ordered read sets (e.g. all barcode 1 reads at the start of a file, followed by barcode 2 reads, etc).</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown"><span class="p">*</span> Many ONT adapters share common sequence with each other, making false positive adapter finds possible.</span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="markdown">A simpler solution (and in hindsight what I should have done) would be to require the kit and/or adapters from the user. E.g. <span class="sb" style="color: #d14;">`porechop --sqk-lsk109`</span> or <span class="sb" style="color: #d14;">`porechop --start_adapt ACGCTAGCATACGT`</span>.</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Performance</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="markdown">Porechop uses <span class="p">[</span><span class="nv" style="color: teal;">SeqAn</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/seqan/seqan</span><span class="p">)</span> to perform its alignments in C++. This library is very flexible, but not as fast as some alternatives, such as <span class="p">[</span><span class="nv" style="color: teal;">Edlib</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/Martinsos/edlib</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="markdown">Another performance issue is that Porechop uses <span class="p">[</span><span class="nv" style="color: teal;">ctypes</span><span class="p">](</span><span class="sx" style="color: #d14;">https://docs.python.org/3/library/ctypes.html</span><span class="p">)</span> to interface with its C++ code. Function calls with ctypes can have a bit of overhead, which means that Porechop cannot use threads very efficiently (it spends too much of its time in the Python code, which is intrinsically non-parallel).</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Barcode demultiplexing</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="markdown">I added demultiplexing to Porechop as an afterthought – it was already looking for barcodes to trim, so why not sort reads by barcodes too? This turned out to be a very useful feature, but in hindsight I think it might be simpler (and easier to maintain) if trimming and demultiplexing functionality were in separate tools.</span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Base-space problems</span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="markdown">I've encountered a couple of issues where adapter sequences are not properly basecalled, resulting in inconsistent sequence. Porechop trims in base-space, so this is a somewhat intractable problem. See <span class="p">[</span><span class="nv" style="color: teal;">issue #40</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/rrwick/Porechop/issues/40</span><span class="p">)</span> for an example.</span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="markdown">These have made me wonder if the adapter trimming should be done in signal-space instead, though that would be a more complex problem to solve. I hope that in the future ONT can integrate this kind of functionality directly into their basecallers.</span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="markdown"><span class="gh" style="color: #999;"># Acknowledgements</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="markdown">Porechop was inspired by (and largely coded during) <span class="p">[</span><span class="nv" style="color: teal;">Porecamp Australia 2017</span><span class="p">](</span><span class="sx" style="color: #d14;">https://porecamp-au.github.io/</span><span class="p">)</span>. Thanks to the organisers and attendees who helped me realise that a Nanopore adapter trimmer might be a useful tool! I later met David Stoddart from Oxford Nanopore at London Calling 2017, and he helped me get many of the adapter sequences right.</span>
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<li id="ed6e4c64fbfbb74aca7c1f7ae77cea47abb8c6f3">
<a href="https://salsa.debian.org/med-team/porechop/commit/9904cd8bf255135b069354758622ae612466aa0b#ed6e4c64fbfbb74aca7c1f7ae77cea47abb8c6f3"><strong>porechop/adapters.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">@@ -43,7 +43,9 @@ class Adapter(object):</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> Gets the barcode name for the output files. We want a concise name, so it looks at all</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> options and chooses the shortest.</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">possible_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">possible_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">possible_names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">possible_names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">barcode_name</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;">possible_names</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,28 +78,36 @@ ADAPTERS = [Adapter('SQK-NSK007',</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-NSK007_Y_Top'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AATGTACTTCGTTCAGTTACGTATTGCT'</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-NSK007_Y_Bottom'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCAATACGTAACTGAACGAAGT'</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'Rapid'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Rapid_adapter'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'Rapid_adapter'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="s" style="color: #d14;">'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'RBK004_upstream'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'RBK004_upstream'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AATGTACTTCGTTCAGTTACGGCTTGGGTGTTTAACC'</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006_Y_Top_SK63'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GGTTGTTTCTGTTGGTGCTGATATTGCT'</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006_Y_Bottom_SK64'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCAATATCAGCACCAACAGAAA'</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006_Y_Top_SK63'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GGTTGTTTCTGTTGGTGCTGATATTGCT'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006_Y_Bottom_SK64'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GCAATATCAGCACCAACAGAAA'</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006 <span class="idiff left right">S</span>hort'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006 <span class="idiff left right">s</span>hort'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006_Short_Y_Top_LI32'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CGGCGTCTGCTTGGGTGTTTAACCT'</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'SQK-MAP006_Short_Y_Bottom_LI33'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GGTTAAACACCCAAGCAGACGCCG'</span><span class="p">)),</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The PCR adapters are used both in PCR DNA kits and some cDNA kits.</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR adapters 1'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR_1_start'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ACTTGCCTGTCGCTCTATCTTC'</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'PCR_1_end'</span><span class="p">,</span> <span class="s" style="color: #d14;">'GAAGATAGAGCGACAGGCAAGT'</span><span class="p">)),</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'PCR_1_end'</span><span class="p">,</span> <span class="idiff left right"> </span><span class="s" style="color: #d14;">'GAAGATAGAGCGACAGGCAAGT'</span><span class="p">)),</span></span>
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR <span class="idiff left right">tail 1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">tail_1_start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'TTAACC</span>TTTCTGTTGGTGCTGATATTGC'</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">tail_1_end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'GCAATATCAGCACCAACAGAAAGGTT</span>AA'</span><span class="p">)),</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR <span class="idiff left right">adapters 2</span>'</span><span class="p">,</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">2_start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>TTTCTGTTGGTGCTGATATTGC'</span><span class="p">),</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">2_end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'GCAATATCAGCACCAACAGA</span>AA'</span><span class="p">)),</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR <span class="idiff left right">tail 2</span>'</span><span class="p">,</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">tail_2_start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'TTAACC</span>TACTTGCCTGTCGCTCTATCTTC'</span><span class="p">),</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">tail_2_end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'GAAGATAGAGCGACAGGCAAGTAGGTTA</span>A'</span><span class="p">)),</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR <span class="idiff left right">adapters 3</span>'</span><span class="p">,</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">3_start'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'</span>TACTTGCCTGTCGCTCTATCTTC'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'PCR_<span class="idiff left">3_end'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'GAAGATAGAGCGACAGGCAAGT</span>A'</span><span class="p">)),</span></span>
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101
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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102
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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103
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 1D^2 kit adapters are interesting. ONT provided the following sequences on their site:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,6 +127,11 @@ ADAPTERS = [Adapter('SQK-NSK007',</td>
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117
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127
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># adapter sequences here.</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'cDNA SSP'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'cDNA_SSP'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TTTCTGTTGGTGCTGATATTGCTGCCATTACGGCCGGG'</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'cDNA_SSP_rev'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CCCGGCCGTAATGGCAGCAATATCAGCACCAACAGAAA'</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Some barcoding kits (like the native barcodes) use the rev comp barcode at the start</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># of the read and the forward barcode at the end of the read.</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'Barcode 1 (reverse)'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -461,11 +476,23 @@ def make_full_native_barcode_adapter(barcode_num):</td>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'NB'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%02</span><span class="s" style="color: #d14;">d'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">barcode_num</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_end'</span><span class="p">,</span> <span class="n" style="color: #333;">end_full_seq</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC464" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_full_rapid_barcode_adapter</span><span class="p">(</span><span class="n" style="color: #333;">barcode_num</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_old_full_rapid_barcode_adapter</span><span class="p">(</span><span class="n" style="color: #333;">barcode_num</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># applies to SQK-RBK001</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"> <span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</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;">ADAPTERS</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Barcode '</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;">barcode_num</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' (forward)'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">start_barcode_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"> <span class="n" style="color: #333;">start_full_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'AATGTACTTCGTTCAGTTACG'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'TATTGCT'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start_barcode_seq</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"> <span class="s" style="color: #d14;">'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'</span></span>
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'Rapid barcoding '</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;">barcode_num</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' (full sequence, old)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'RB'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%02</span><span class="s" style="color: #d14;">d'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">barcode_num</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_full'</span><span class="p">,</span> <span class="n" style="color: #333;">start_full_seq</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_new_full_rapid_barcode_adapter</span><span class="p">(</span><span class="n" style="color: #333;">barcode_num</span><span class="p">):</span> <span class="c1" style="color: #998; font-style: italic;"># applies to SQK-RBK004</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">barcode</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</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;">ADAPTERS</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'Barcode '</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;">barcode_num</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' (forward)'</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">start_barcode_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">barcode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="python"> <span class="n" style="color: #333;">start_full_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'AATGTACTTCGTTCAGTTACGTATTGCT'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start_barcode_seq</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'</span></span>
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">start_full_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'AATGTACTTCGTTCAGTTACG'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'GCTTGGGTGTTTAACC'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">start_barcode_seq</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="s" style="color: #d14;">'GTTTTCGCATTTATCGTGAAACGCTTTCGCGTTTTTCGTGCGCCGCTTCA'</span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'Rapid barcoding '</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;">barcode_num</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' (full sequence)'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'Rapid barcoding '</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;">barcode_num</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' (full sequence<span class="idiff left right">, new</span>)'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'RB'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%02</span><span class="s" style="color: #d14;">d'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">barcode_num</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'_full'</span><span class="p">,</span> <span class="n" style="color: #333;">start_full_seq</span><span class="p">))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/porechop/commit/9904cd8bf255135b069354758622ae612466aa0b#bcc6990bda499ad6312bebe6fa27eddcd005e148"><strong>porechop/nanopore_read.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">@@ -23,7 +23,13 @@ class NanoporeRead(object):</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">quals</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC24" 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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" 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;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span></span>
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<pre style="margin: 0;">+<span id="LC26" 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;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'U'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'T'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC28" 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;">rna</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC29" 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;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</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;">'U'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC31" 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;">rna</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" 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;">quals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quals</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">)</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;">seq</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC35" 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;">quals</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="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</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;">quals</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,6 +102,8 @@ class NanoporeRead(object):</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_seq_with_start_end_adapters_trimmed</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC103" 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;">seq</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Don't return empty sequences</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rna</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</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;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'U'</span><span class="p">)</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</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="n" style="color: #333;">add_line_breaks_to_sequence</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="mi" style="color: #099;">70</span><span class="p">)])</span></span>
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">discard_middle</span><span class="p">:</span></span>
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101
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">''</span></span>
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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="114" style="width: 35px; color: rgba(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 +114,8 @@ class NanoporeRead(object):</td>
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106
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<td class="diff-line-num new_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
114
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<pre style="margin: 0;"> <span id="LC114" 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;">split_read_part</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span> <span class="c1" style="color: #998; font-style: italic;"># Don't return empty sequences</span></span>
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107
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">''</span></span>
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108
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116
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_line_breaks_to_sequence</span><span class="p">(</span><span class="n" style="color: #333;">split_read_part</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="mi" style="color: #099;">70</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rna</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</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;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'U'</span><span class="p">)</span></span>
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109
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">fasta_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="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</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="n" style="color: #333;">seq</span><span class="p">])</span></span>
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110
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fasta_str</span></span>
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111
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121
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="119" style="width: 35px; color: rgba(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="129" style="width: 35px; color: rgba(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">@@ -119,6 +129,8 @@ class NanoporeRead(object):</td>
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119
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">quals</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_quals_with_start_end_adapters_trimmed</span><span class="p">()</span></span>
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120
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130
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<pre style="margin: 0;"> <span id="LC130" 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;">seq</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Don't return empty sequences</span></span>
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121
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">''</span></span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rna</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</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;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'U'</span><span class="p">)</span></span>
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122
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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="s" style="color: #d14;">'@'</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</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="n" style="color: #333;">seq</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">quals</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>
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123
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">discard_middle</span><span class="p">:</span></span>
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124
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136
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">''</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,10 +138,12 @@ class NanoporeRead(object):</td>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">fastq_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">split_read_part</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_split_read_parts</span><span class="p">(</span><span class="n" style="color: #333;">min_split_read_size</span><span class="p">)):</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_number_to_read_name</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">i</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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129
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<pre style="margin: 0;">-<span id="LC129" 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;">split_read_part</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span> <span class="c1" style="color: #998; font-style: italic;"># Don't return empty sequences</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split_read_part</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">split_read_part</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC142" 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;">seq</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Don't return empty sequences</span></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">fastq_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="s" style="color: #d14;">'@'</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</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="n" style="color: #333;">split_read_part</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</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>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">split_read_part</span><span class="p">[</span><span class="mi" style="color: #099;">1</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>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rna</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</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;">'T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'U'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">fastq_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="s" style="color: #d14;">'@'</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</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="n" style="color: #333;">seq</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="n" style="color: #333;">qual</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>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fastq_str</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">align_adapter_set</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_set</span><span class="p">,</span> <span class="n" style="color: #333;">end_size</span><span class="p">,</span> <span class="n" style="color: #333;">scoring_scheme_vals</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,10 +152,11 @@ class NanoporeRead(object):</td>
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138
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"><span class="s" style="color: #d14;"> This is not to determine where to trim the reads, but rather to figure out which adapter</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"><span class="s" style="color: #d14;"> sets are present in the data.</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">read_seq_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">[:</span><span class="n" style="color: #333;">end_size</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align_adapter</span><span class="p">(</span><span class="n" style="color: #333;">read_seq_start</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">scoring_scheme_vals</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_score</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">read_seq_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">[:</span><span class="n" style="color: #333;">end_size</span><span class="p">]</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align_adapter</span><span class="p">(</span><span class="n" style="color: #333;">read_seq_start</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">scoring_scheme_vals</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_score</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_score</span><span class="p">,</span> <span class="n" style="color: #333;">score</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">read_seq_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">end_size</span><span class="p">:]</span></span>
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147
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">score</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">align_adapter</span><span class="p">(</span><span class="n" style="color: #333;">read_seq_end</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -156,6 +171,8 @@ class NanoporeRead(object):</td>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">read_seq_start</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">[:</span><span class="n" style="color: #333;">end_size</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">adapter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapters</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC174" 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;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">:</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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159
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">full_score</span><span class="p">,</span> <span class="n" style="color: #333;">partial_score</span><span class="p">,</span> <span class="n" style="color: #333;">read_start</span><span class="p">,</span> <span class="n" style="color: #333;">read_end</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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160
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">align_adapter</span><span class="p">(</span><span class="n" style="color: #333;">read_seq_start</span><span class="p">,</span> <span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">scoring_scheme_vals</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">partial_score</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">end_threshold</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">read_end</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">end_size</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<a href="https://salsa.debian.org/med-team/porechop/commit/9904cd8bf255135b069354758622ae612466aa0b#b3c5c58de7161317c864b8c5319db46fb841057a"><strong>porechop/porechop.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">@@ -24,7 +24,8 @@ import re</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing.dummy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Pool</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ThreadPool</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.misc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">load_fasta_or_fastq</span><span class="p">,</span> <span class="n" style="color: #333;">print_table</span><span class="p">,</span> <span class="n" style="color: #333;">red</span><span class="p">,</span> <span class="n" style="color: #333;">bold_underline</span><span class="p">,</span> <span class="n" style="color: #333;">MyHelpFormatter</span><span class="p">,</span> <span class="n" style="color: #333;">int_to_str</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ADAPTERS</span><span class="p">,</span> <span class="n" style="color: #333;">make_full_native_barcode_adapter</span><span class="p">,</span> <span class="n" style="color: #333;">make_full_rapid_barcode_adapter</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ADAPTERS</span><span class="p">,</span> <span class="n" style="color: #333;">make_full_native_barcode_adapter</span><span class="p">,</span>\</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">make_old_full_rapid_barcode_adapter</span><span class="p">,</span> <span class="n" style="color: #333;">make_new_full_rapid_barcode_adapter</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.nanopore_read</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">NanoporeRead</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></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">@@ -37,16 +38,17 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_matching_adapter_sets</span><span class="p">(</span><span class="n" style="color: #333;">check_reads</span><span class="p">,</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="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_size</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" 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;">scoring_scheme_vals</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_dest</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC40" 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;">adapter_threshold</span><span class="p">,</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="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exclude_end_adapters_for_rapid</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fix_up_1d2_sets</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">display_adapter_set_results</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">,</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="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_full_barcode_adapter_sets</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" 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;">barcode_dir</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">forward_or_reverse_barcodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">choose_barcoding_kit</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">,</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="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC45" 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;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">forward_or_reverse_barcodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">display_adapter_set_results</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">,</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="p">,</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_full_barcode_adapter_sets</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" 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>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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="nb" style="color: #0086b3;">file</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;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></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">@@ -86,7 +88,7 @@ def get_arguments():</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Porechop: a tool for finding adapters in Oxford '</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="s" style="color: #d14;">'Nanopore reads, trimming them from the ends and '</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">'splitting reads with internal adapters'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">MyHelpFormatter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">formatter_class</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">MyHelpFormatter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">add_help</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">False</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">main_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;">'Main options'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">main_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;">'-i'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--input'</span><span class="p">,</span> <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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94
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<pre style="margin: 0;"> <span id="LC94" 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;">'FASTA/FASTQ of input reads or a directory which will be '</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,7 +107,6 @@ def get_arguments():</td>
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105
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'a file and stderr if reads are printed to stdout'</span><span class="p">)</span></span>
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106
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">main_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;">'-t'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--threads'</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 class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default_threads</span><span class="p">,</span></span>
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107
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109
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<pre style="margin: 0;"> <span id="LC109" 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;">'Number of threads to use for adapter alignment'</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">main_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;">'--version'</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;">'version'</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;">__version__</span><span class="p">)</span></span>
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109
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">barcode_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;">'Barcode binning settings'</span><span class="p">,</span></span>
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111
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">'Control the binning of reads based on barcodes '</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="128" style="width: 35px; color: rgba(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">@@ -127,8 +128,7 @@ def get_arguments():</td>
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127
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">'match for the barcode on both their start and end (default: '</span></span>
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128
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="s" style="color: #d14;">'a read can be binned with a match at its start or end)'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">barcode_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;">'--untrimmed'</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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130
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<pre style="margin: 0;">-<span id="LC130" 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;">'Bin reads but do not trim them (appropriate if reads are to '</span></span>
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131
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="s" style="color: #d14;">'be used with Nanopolish) (default: trim the reads)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC131" 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;">'Bin reads but do not trim them (default: trim the reads)'</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">barcode_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;">'--discard_unassigned'</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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133
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133
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<pre style="margin: 0;"> <span id="LC133" 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;">'Discard unassigned reads (instead of creating a "none" bin)'</span><span class="p">)</span></span>
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134
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="169" style="width: 35px; color: rgba(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">@@ -169,9 +169,10 @@ def get_arguments():</td>
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169
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="s" style="color: #d14;">'middle)'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">middle_trim_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;">'--discard_middle'</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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<pre style="margin: 0;"> <span id="LC171" 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;">'Reads with middle adapters will be discarded (default: '</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">'reads with middle adapters are split) (this option is '</span></span>
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">'on by default when outputting reads into barcode bins)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">middle_trim_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;">'--middle_threshold'</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;">float</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">85.0</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">'reads with middle adapters are split) (required for '</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">'reads to be used with Nanopolish, this option is on by '</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">'default when outputting reads into barcode bins)'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">middle_trim_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;">'--middle_threshold'</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;">float</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">90.0</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC176" 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;">'Adapters in the middle of reads must have at least this '</span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="s" style="color: #d14;">'percent identity to be found (0 to 100)'</span><span class="p">)</span></span>
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">middle_trim_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;">'--extra_middle_trim_good_side'</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 class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">10</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,6 +185,12 @@ def get_arguments():</td>
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<pre style="margin: 0;"> <span id="LC185" 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;">'Post-split read pieces smaller than this many base pairs '</span></span>
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="s" style="color: #d14;">'will not be outputted'</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">help_args</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;">'Help'</span><span class="p">)</span></span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">help_args</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;">'-h'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--help'</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;">'help'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">argparse</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">,</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Show this help message and exit'</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">help_args</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;">'--version'</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;">'version'</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;">__version__</span><span class="p">,</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" 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;">"Show program's version number and exit"</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC194" 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;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -325,35 +332,43 @@ def choose_barcoding_kit(adapter_sets, verbosity, print_dest):</td>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"><span class="s" style="color: #d14;"> If the user is sorting reads by barcode bin, choose one barcode configuration (rev comp</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"><span class="s" style="color: #d14;"> barcodes at the start of the read or at the end of the read) and ignore the other.</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">forward_barcodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">reverse_barcodes</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Tally up scores for forward and reverse barcodes.</span></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="n" style="color: #333;">forward_start_or_end</span><span class="p">,</span> <span class="n" style="color: #333;">reverse_start_or_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">forward_start_and_end</span><span class="p">,</span> <span class="n" style="color: #333;">reverse_start_and_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">adapter_set</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_sets</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_or_end_score</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'Barcode'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'(forward)'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">forward_barcodes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'Barcode'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'(reverse)'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="n" style="color: #333;">reverse_barcodes</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">score</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">forward_barcodes</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">reverse_barcodes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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;">Barcodes determined to be in forward orientation'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'forward'</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">reverse_barcodes</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">forward_barcodes</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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;">Barcodes determined to be in reverse orientation'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'reverse'</span></span>
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'barcode'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'(forward)'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">forward_start_or_end</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_or_end_score</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="n" style="color: #333;">forward_start_and_end</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_score</span></span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">forward_start_and_end</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_end_score</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'(reverse)'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="n" style="color: #333;">reverse_start_or_end</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_or_end_score</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">reverse_start_and_end</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_start_score</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">reverse_start_and_end</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">adapter_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_end_score</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">forward_start_or_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">reverse_start_or_end</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">'Error: no barcodes were found, so Porechop cannot perform barcode demultiplexing'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If possible, make a decision using each barcode's best start OR end score.</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">orientation</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">forward_start_or_end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">reverse_start_or_end</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">orientation</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'forward'</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">reverse_start_or_end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">forward_start_or_end</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">orientation</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'reverse'</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If that didn't work (i.e. it's a tie between forward and reverse), then choose based on the</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># sum of both start AND end scores.</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">forward_start_and_end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">reverse_start_and_end</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">orientation</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'forward'</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">reverse_start_and_end</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">forward_start_and_end</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">orientation</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'reverse'</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">orientation</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">'Error: Porechop could not determine barcode orientation'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">exclude_end_adapters_for_rapid</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;"> Rapid reads shouldn't have end adapters, so we don't want to look for them if this seems to be</span></span>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"><span class="s" style="color: #d14;"> a rapid read set.</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'Rapid adapter'</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="n" style="color: #333;">name</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;">matching_sets</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matching_sets</span><span class="p">:</span></span>
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355
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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356
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matching_sets</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</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;">Barcodes determined to be in '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">orientation</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' orientation'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">orientation</span></span>
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372
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"></span>
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358
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373
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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"></span>
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359
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">fix_up_1d2_sets</span><span class="p">(</span><span class="n" style="color: #333;">matching_sets</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -411,8 +426,11 @@ def add_full_barcode_adapter_sets(matching_sets):</td>
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Rapid barcode full sequences</span></span>
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413
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428
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matching_set_names</span></span>
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414
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<pre style="margin: 0;">-<span id="LC414" 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="s" style="color: #d14;">'SQK-NSK007'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Rapid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Barcode '</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;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' (forward)'</span><span class="p">]):</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</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;">make_full_rapid_barcode_adapter</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" 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="s" style="color: #d14;">'Rapid'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Barcode '</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;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' (forward)'</span><span class="p">]):</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'RBK004_upstream'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matching_set_names</span><span class="p">:</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</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;">make_new_full_rapid_barcode_adapter</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'SQK-NSK007'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matching_set_names</span><span class="p">:</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">matching_sets</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;">make_old_full_rapid_barcode_adapter</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matching_sets</span></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"></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">@@ -424,11 +442,14 @@ def find_adapters_at_read_ends(reads, matching_sets, verbosity, end_size, extra_</td>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">bold_underline</span><span class="p">(</span><span class="s" style="color: #d14;">'Trimming adapters from read ends'</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">name_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</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;">matching_sets</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</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;">matching_sets</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="python"> <span class="n" style="color: #333;">name_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</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;">matching_sets</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</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;">matching_sets</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">matching_set</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matching_sets</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rjust</span><span class="p">(</span><span class="n" style="color: #333;">name_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">': '</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="n" style="color: #333;">red</span><span class="p">(</span><span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rjust</span><span class="p">(</span><span class="n" style="color: #333;">name_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">': '</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="n" style="color: #333;">red</span><span class="p">(</span><span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rjust</span><span class="p">(</span><span class="n" style="color: #333;">name_len</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">': '</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python"> <span class="n" style="color: #333;">red</span><span class="p">(</span><span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">print_dest</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -519,15 +540,18 @@ def find_adapters_in_read_middles(reads, matching_sets, verbosity, middle_thresh</td>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"> <span class="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">matching_set</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matching_sets</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="python"> <span class="n" style="color: #333;">adapters</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;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC523" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span> <span class="ow" style="font-weight: 600;">and</span> \</span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</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;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">adapters</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;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="python"> <span class="n" style="color: #333;">adapters</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;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> \</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</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;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">adapters</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;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">matching_set</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matching_sets</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence_names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">start_sequence_names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"> <span class="n" style="color: #333;">end_sequence_names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">matching_set</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_sequence</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/porechop/commit/9904cd8bf255135b069354758622ae612466aa0b#aea35a4ca593a300f3e36b82cee91a18d2a09955"><strong>porechop/version.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">@@ -2,4 +2,4 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">The version is stored here in a separate file so it can exist in only one place.</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">http://stackoverflow.com/questions/458550</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC5" 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;">'0.2.<span class="idiff left right">3</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" 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;">'0.2.<span class="idiff left right">4</span>'</span></span></pre>
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