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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pycoqc">Debian Med / pycoqc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/41d92f77e0f0bd05af4e51bd9a321a594f297ed8">41d92f77</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-22T11:26:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Override false positives about compressed JS in example output
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/bbf3bbe1384553d27c6d3834cdb496b65e9b48e5">bbf3bbe1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-22T11:59:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix dependencies
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/2a7e7f6f0b1643f2ae77b41ca1f8a953199df643">2a7e7f6f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-04-22T11:59:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#16c57e9357794082d68cde8bfb1dbef11f3c273f">
<span class="new-file">
+
debian/Barcode_split.1
</span>
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</li>
<li class="file-stats">
<a href="#8a615ed88d7804f27145fcb2523c459425b0f95c">
<span class="new-file">
+
debian/Fast5_to_seq_summary.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="new-file">
+
debian/patches/series
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</li>
<li class="file-stats">
<a href="#0aa89a673dddcef13146490f72be3826ee34e931">
<span class="new-file">
+
debian/patches/unversioned_depends_tqdm.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#b88c83fb443c26c9d122a346b303f479e19307b2">
<span class="new-file">
+
debian/pycoQC.1
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</a>
</li>
<li class="file-stats">
<a href="#85ccdeeb03055211183e48520592d9a93592b330">
<span class="new-file">
+
debian/source/lintian-overrides
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="16c57e9357794082d68cde8bfb1dbef11f3c273f">
<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#16c57e9357794082d68cde8bfb1dbef11f3c273f"><strong>debian/Barcode_split.1</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BARCODE_SPLIT "1" "April 2020" "Barcode_split 2.5.0.21" "User Commands"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Barcode_split \- simple tool to split sequencing summary report in per barcodes</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: Barcode_split [\-h] [\-\-version] \fB\-\-summary_file\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[SUMMARY_FILE [SUMMARY_FILE ...]]</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-\-barcode_file [BARCODE_FILE [BARCODE_FILE ...]]]</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-output_dir OUTPUT_DIR] [\-\-output_unclassified]</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">[\-\-min_barcode_percent MIN_BARCODE_PERCENT] [\-v | \fB\-q]\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.PP</span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Barcode_split is a simple tool to split sequencing summary report in per</span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">barcodes</span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">show this help message and exit</span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-\-version\fR</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">show program's version number and exit</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-\-summary_file\fR [SUMMARY_FILE [SUMMARY_FILE ...]], \fB\-f\fR [SUMMARY_FILE [SUMMARY_FILE ...]]</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Path to a sequencing_summary generated by Albacore</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">(guppy_basecaller). One can also pass multiple space</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">separated file paths or a UNIX style regex matching</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">multiple files</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-\-barcode_file\fR [BARCODE_FILE [BARCODE_FILE ...]], \fB\-b\fR [BARCODE_FILE [BARCODE_FILE ...]]</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Path to the barcode_file generated by Guppy 2.1.3+</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">(guppy_barcoder) or Deepbinner 0.2.0+. One can also</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">pass multiple space separated file paths or a UNIX</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">style regex matching multiple files</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-\-output_dir\fR OUTPUT_DIR, \fB\-o\fR OUTPUT_DIR</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Folder where to output split barcode data (default:</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">current dir</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-\-output_unclassified\fR, \fB\-u\fR</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">If given, unclassified barcodes are also written in a</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">file. By default they are skiped</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-\-min_barcode_percent\fR MIN_BARCODE_PERCENT, \fB\-p\fR MIN_BARCODE_PERCENT</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Minimal percent of total reads to retain barcode</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">label. If below, the barcode value is set as</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">`unclassified` (default: 0.1)</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.TP</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-verbose\fR</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Increase verbosity</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-q\fR, \fB\-\-quiet\fR</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Reduce verbosity</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="8a615ed88d7804f27145fcb2523c459425b0f95c">
<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#8a615ed88d7804f27145fcb2523c459425b0f95c"><strong>debian/Fast5_to_seq_summary.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FAST5_TO_SEQ_SUMMARY "1" "April 2020" "Fast5_to_seq_summary 2.5.0.21" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Fast5_to_seq_summary \- generate a sequencing summary like file from a directory containing Fast5 files</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: Fast5_to_seq_summary [\-h] [\-\-version] \fB\-\-fast5_dir\fR FAST5_DIR</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">\fB\-\-seq_summary_fn\fR SEQ_SUMMARY_FN</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-\-max_fast5 MAX_FAST5] [\-\-threads THREADS]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-basecall_id BASECALL_ID]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">[\-\-fields FIELDS [FIELDS ...]] [\-\-include_path]</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">[\-\-verbose_level VERBOSE_LEVEL]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Fast5_to_seq_summary generate a sequencing summary like file from a directory</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">containing Fast5 files</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "optional arguments:"</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">show this help message and exit</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-\-version\fR, \fB\-v\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">show program's version number and exit</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-\-fast5_dir\fR FAST5_DIR, \fB\-f\fR FAST5_DIR</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Directory containing fast5 files. Can contain multiple</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">subdirectories</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-\-seq_summary_fn\fR SEQ_SUMMARY_FN, \fB\-s\fR SEQ_SUMMARY_FN</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">path of the summary sequencing file where to write the</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">data extracted from the fast5 files</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-\-max_fast5\fR MAX_FAST5</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Maximum number of file to try to parse. 0 to</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">deactivate (default: 0)</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-\-threads\fR THREADS, \fB\-t\fR THREADS</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Total number of threads to use. 1 thread is used for</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">the reader and 1 for the writer. Minimum 3 (default:</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">4)</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-\-basecall_id\fR BASECALL_ID</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">id of the basecalling group. By default leave to 0,</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">but if you perfome multiple basecalling on the same</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">fast5 files, this can be used to indicate the</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">corresponding group (1, 2 ...) (default: 0)</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-\-fields\fR FIELDS [FIELDS ...]</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">list of field names corresponding to attributes to try</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">to fetch from the fast5 files (default: ['read_id',</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\&'run_id', 'channel', 'start_time',</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\&'sequence_length_template', 'mean_qscore_template',</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\&'calibration_strand_genome_template',</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\&'barcode_arrangement'])</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">\fB\-\-include_path\fR</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">If given, the absolute path to the corresponding file</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">is added in an extra column (default: False)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-\-verbose_level\fR VERBOSE_LEVEL</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">Level of verbosity, from 2 (Chatty) to 0 (Nothing)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">(default: 0)</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -15,7 +15,15 @@ Homepage: https://github.com/a-slide/pycoQC</td>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: pycoqc</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python3-numpy,</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> python3-scipy,</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3-pandas,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> python3-plotly (>= 4.1.0),</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python3-jinja2,</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-h5py,</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> python3-tqdm,</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> python3-pysam</span>
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19
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Description: computes metrics and generates Interactive QC plots</span>
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20
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> PycoQC computes metrics and generates interactive QC plots for Oxford</span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> Nanopore technologies sequencing data</span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>pycoQC</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"computes metrics and generates interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecallers"</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>Fast5_to_seq_summary</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"generate a sequencing summary like file from a directory containing Fast5 files"</span> <span class="se" style="color: #d14;">\</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>Barcode_split</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" --help"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"simple tool to split sequencing summary report in per barcodes"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">unversioned_depends_tqdm.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#0aa89a673dddcef13146490f72be3826ee34e931"><strong>debian/patches/unversioned_depends_tqdm.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Wed, 22 Apr 2020 09:21:46 +0200</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Do not check for absolute equality of tqdm</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/setup.py</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -34,7 +34,7 @@</span> setup(</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> 'plotly==4.1.0',</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> 'jinja2==2.10.1',</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> 'h5py==2.9.0',</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- 'tqdm==4.35.0',</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ 'tqdm>=4.35.0',</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> 'pysam==0.15.3'],</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> packages = [name],</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> package_dir = {name: name},</span></pre>
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<li id="b88c83fb443c26c9d122a346b303f479e19307b2">
<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#b88c83fb443c26c9d122a346b303f479e19307b2"><strong>debian/pycoQC.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.13.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH PYCOQC "1" "April 2020" "pycoQC 2.5.0.21" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">pycoQC \- computes metrics and generates interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecallers</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: pycoQC [\-h] [\-\-version]</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.IP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[\-\-summary_file [SUMMARY_FILE [SUMMARY_FILE ...]]]</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-\-barcode_file [BARCODE_FILE [BARCODE_FILE ...]]]</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-bam_file [BAM_FILE [BAM_FILE ...]]]</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">[\-\-html_outfile HTML_OUTFILE] [\-\-json_outfile JSON_OUTFILE]</span>
</pre>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">[\-\-min_pass_qual MIN_PASS_QUAL] [\-\-min_pass_len MIN_PASS_LEN]</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">[\-\-filter_calibration] [\-\-filter_duplicated]</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">[\-\-min_barcode_percent MIN_BARCODE_PERCENT]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">[\-\-report_title REPORT_TITLE] [\-\-template_file TEMPLATE_FILE]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">[\-\-config_file CONFIG_FILE] [\-\-sample SAMPLE] [\-\-default_config]</span>
</pre>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">[\-v | \fB\-q]\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.PP</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">pycoQC computes metrics and generates interactive QC plots from the sequencing summary</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">report generated by Oxford Nanopore technologies basecallers</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.PP</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">* Minimal usage</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">pycoQC \fB\-f\fR sequencing_summary.txt \fB\-o\fR pycoQC_output.html</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.PP</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">* Including Guppy barcoding file + html output + json output</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">pycoQC \fB\-f\fR sequencing_summary.txt \fB\-b\fR barcoding_sequencing.txt \fB\-o\fR pycoQC_output.html \fB\-j\fR pycoQC_output.json</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">* Including Bam file + html output</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">pycoQC \fB\-f\fR sequencing_summary.txt \fB\-a\fR alignment.bam \fB\-o\fR pycoQC_output.html</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.SS "optional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-\-version\fR</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">show program's version number and exit</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-verbose\fR</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Increase verbosity</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-q\fR, \fB\-\-quiet\fR</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Reduce verbosity</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.SS "Input/output options:"</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-\-summary_file\fR [SUMMARY_FILE [SUMMARY_FILE ...]], \fB\-f\fR [SUMMARY_FILE [SUMMARY_FILE ...]]</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Path to a sequencing_summary generated by Albacore</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">1.0.0 + (read_fast5_basecaller.py) / Guppy 2.1.3+</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">(guppy_basecaller). One can also pass multiple space</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">separated file paths or a UNIX style regex matching</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">multiple files (Required)</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">\fB\-\-barcode_file\fR [BARCODE_FILE [BARCODE_FILE ...]], \fB\-b\fR [BARCODE_FILE [BARCODE_FILE ...]]</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Path to the barcode_file generated by Guppy 2.1.3+</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">(guppy_barcoder) or Deepbinner 0.2.0+. This is not a</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">required file. One can also pass multiple space</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">separated file paths or a UNIX style regex matching</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">multiple files (optional)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">\fB\-\-bam_file\fR [BAM_FILE [BAM_FILE ...]], \fB\-a\fR [BAM_FILE [BAM_FILE ...]]</span>
</pre>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">Path to a Bam file corresponding to reads in the</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">summary_file. Preferably aligned with Minimap2 One can</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">also pass multiple space separated file paths or a</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">UNIX style regex matching multiple files (optional)</span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-\-html_outfile\fR HTML_OUTFILE, \fB\-o\fR HTML_OUTFILE</span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">Path to an output html file report (required if</span>
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<td class="diff-line-num new new_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">json_outfile not given)</span>
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<td class="diff-line-num new new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-\-json_outfile\fR JSON_OUTFILE, \fB\-j\fR JSON_OUTFILE</span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">Path to an output json file report (required if</span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">html_outfile not given)</span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.SS "Filtering options:"</span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">\fB\-\-min_pass_qual\fR MIN_PASS_QUAL</span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">Minimum quality to consider a read as 'pass' (default:</span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">7)</span>
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<td class="diff-line-num new new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">\fB\-\-min_pass_len\fR MIN_PASS_LEN</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">Minimum read length to consider a read as 'pass'</span>
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<td class="diff-line-num new new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">(default: 0)</span>
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<td class="diff-line-num new new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">\fB\-\-filter_calibration\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">If given, reads flagged as calibration strand by the</span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">basecaller are removed (default: False)</span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">\fB\-\-filter_duplicated\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">If given, duplicated read_ids are removed but the</span>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">first occurence is kept (Guppy sometimes outputs the</span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">same read multiple times) (default: False)</span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">\fB\-\-min_barcode_percent\fR MIN_BARCODE_PERCENT</span>
</pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">Minimal percent of total reads to retain barcode</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">label. If below, the barcode value is set as</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">`unclassified` (default: 0.1)</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">.SS "HTML report options:"</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">.TP</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-\-report_title\fR REPORT_TITLE</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">Title to use in the html report (default: PycoQC</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">report)</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">.TP</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">\fB\-\-template_file\fR TEMPLATE_FILE</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">Jinja2 html template for the html report (default: )</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.TP</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">\fB\-\-config_file\fR CONFIG_FILE</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">Path to a JSON configuration file for the html report.</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">If not provided, looks for it in ~/.pycoQC and</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">~/.config/pycoQC/config. If it's still not found,</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">falls back to default parameters. The first level keys</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">are the names of the plots to be included. The second</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">level keys are the parameters to pass to each plotting</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">function (default: )")</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">.SS "Other options:"</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.TP</span>
</pre>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">\fB\-\-sample\fR SAMPLE</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">If not None a n number of reads will be randomly</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">selected instead of the entire dataset for ploting</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">function (deterministic sampling) (default: 100000)</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">.TP</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">\fB\-\-default_config\fR, \fB\-d\fR</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">Print default configuration file. Can be used to</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">generate a template JSON file (default: False)</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/47825e4911720bef440d3fd13a595364d197d9e6...2a7e7f6f0b1643f2ae77b41ca1f8a953199df643#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># The rendered sample results are no JS without source</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">pycoqc source: source-is-missing docs/pycoQC/results*</span></pre>
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