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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/fast5-research">Debian Med / fast5-research</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0">d514d956</a></strong>
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<span>by Shayan Doust</span>
<i>at 2020-08-04T20:22:26+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manual pages for the scripts, remove lintian overrides and prevent sphinx from generating the manpage
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<h4>8 changed files:</h4>
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debian/fast5-research.lintian-overrides
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<a href="#d99723922c51119b91b003c0612bc22a015a0436">
debian/fast5-research.manpages
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debian/mans/extract_reads.1
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debian/mans/filter_from_bam.1
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debian/mans/filter_reads.1
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debian/mans/index_reads.1
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debian/mans/read_summary.1
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="a0adc3f167ffc17d3dbcfc17420b921dedd715cc">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#a0adc3f167ffc17d3dbcfc17420b921dedd715cc"><strong>debian/fast5-research.lintian-overrides</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># The following relevant binaries are documented within sphinx generated "man fast5_research"</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">fast5-research: no-manual-page usr/bin/filter_from_bam</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">fast5-research: no-manual-page usr/bin/filter_reads</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">fast5-research: no-manual-page usr/bin/index_reads</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">fast5-research: no-manual-page usr/bin/read_summary</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">fast5-research: no-manual-page usr/bin/extract_reads</span></pre>
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<li id="d99723922c51119b91b003c0612bc22a015a0436">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#d99723922c51119b91b003c0612bc22a015a0436"><strong>debian/fast5-research.manpages</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">build/man/*</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">debian/mans/*.1</span></span></pre>
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<li id="1609da36a127c4e2f706ee8c5315ca4e2a8dfd87">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#1609da36a127c4e2f706ee8c5315ca4e2a8dfd87"><strong>debian/mans/extract_reads.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 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH EXTRACT_READS "1" "August 2020" "fast5-research" "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">extract_reads \- extract reads from a bulk .fast5</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">Extracts reads from a bulk .fast5 to either single or multi-read .fast5</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">extract_reads [\-h] [\-\-multi | \fB\-\-single]\fR [\-\-flat] [\-\-by_id] [\-\-prefix PREFIX] [\-\-channel_range CHANNEL_RANGE CHANNEL_RANGE] [\-\-summary SUMMARY] [\-\-workers WORKERS] [\-\-limit LIMIT]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">input output</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">input</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.br</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Bulk .fast5 file for input.</span>
</pre>
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</tr>
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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">.TP</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">output</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.br</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="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="plaintext">Output folder.</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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.SS "optional arguments:"</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
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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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
</pre>
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</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<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="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 this help message and exit</span>
</pre>
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</tr>
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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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="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">
</td>
<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-\-multi\fR</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Output multi\-read files.</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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-\-single\fR</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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Output single\-read files.</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
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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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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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="LC30" class="line" lang="plaintext">\fB\-\-flat\fR</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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Create all .fast5 files in one directory</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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-\-by_id\fR</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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Name single\-read .fast5 files by read_id.</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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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="LC35" class="line" lang="plaintext">.TP</span>
</pre>
</td>
</tr>
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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="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-\-prefix\fR PREFIX</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Read file prefix.</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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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="LC38" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-\-channel_range\fR CHANNEL_RANGE CHANNEL_RANGE</span>
</pre>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Channel range (inclusive).</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-summary\fR SUMMARY</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Strand summary file containing at least columns</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">channel, start_time and duration).</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">\fB\-\-workers\fR WORKERS</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">Number of worker processes.</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\-\-limit\fR LIMIT</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Limit reads per channel.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">[\-\-prefix PREFIX]</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">[\-\-channel_range CHANNEL_RANGE CHANNEL_RANGE]</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">[\-\-summary SUMMARY] [\-\-workers WORKERS] [\-\-limit LIMIT]</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">input output</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"></span></pre>
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<li id="0eb162906194e13950be4885612c7baa406a7ac6">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#0eb162906194e13950be4885612c7baa406a7ac6"><strong>debian/mans/filter_from_bam.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH FILTER_FROM_BAM "1" "August 2020" "fast5-research" "User Commands"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">filter_from_bam \- create filter file from BAM and sequencing summary</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">filter_from_bam [\-h] [\-\-seperator SEP] [\-\-id\-col READID_COL] [\-\-fname\-col FNAME_COL] [\-r REGION] [\-\-workers WORKERS] [\-p] BAM SUMMARY [SUMMARY ...]</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.SS "positional arguments:"</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
</pre>
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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">BAM</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.br</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Path to BAM file</span>
</pre>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">SUMMARY</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.br</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Sequencing summary files</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">.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">
16
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<pre style="margin: 0;">+<span id="LC16" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">show this help message and exit</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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-\-seperator\fR SEP</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Separator in sequencing summary files</span>
</pre>
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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">.TP</span>
</pre>
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</tr>
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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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-\-id\-col\fR READID_COL</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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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Column name for read_id in sequencing summary files</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="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
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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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-\-fname\-col\fR FNAME_COL</span>
</pre>
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</tr>
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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="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Column name for fast5 filename in sequencing summary</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">files</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
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</tr>
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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="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-r\fR REGION, \fB\-\-region\fR REGION</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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Print reads only from this region</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="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-\-workers\fR WORKERS</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="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Number of worker processes.</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-p\fR, \fB\-\-primary\-only\fR</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Ignore secondary and supplementary alignments</span></pre>
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<li id="d2918bfeeb2c239667ac4908f09fcfd70f8d1a48">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#d2918bfeeb2c239667ac4908f09fcfd70f8d1a48"><strong>debian/mans/filter_reads.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 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH FILTER_READS "1" "August 2020" "fast5-research" "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">filter_reads \- extract reads from multi\-read .fast5 files </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">filter_reads [\-h] [\-\-tsv_field TSV_FIELD] [\-\-prefix PREFIX] [\-\-recursive] [\-\-workers WORKERS] [\-\-multi | \fB\-\-single]\fR input output filter</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Extract reads from multi\-read .fast5 files.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS "positional arguments:"</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">input</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Path to input multi\-read .fast5 files (or list of</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">files).</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">output</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Output folder.</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">filter</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">A .tsv file with column `read_id` defining required</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">reads. If a `filename` column is present, this will be</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">used as the location of the read.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.SS "optional arguments:"</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">show this help message and exit</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.TP</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">\fB\-\-tsv_field\fR TSV_FIELD</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Field name from `filter` file to obtain read IDs.</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-\-prefix\fR PREFIX</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Read file prefix.</span>
</pre>
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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\-\-recursive\fR</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">Search recursively under `input` for source files.</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-\-workers\fR WORKERS</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Number of worker processes.</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.TP</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">\fB\-\-multi\fR</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Output multi\-read files.</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-\-single\fR</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Output single\-read files.</span></pre>
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</table>
<br>
</li>
<li id="49596fd435c66e42f40f01a2742dff05015d165c">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#49596fd435c66e42f40f01a2742dff05015d165c"><strong>debian/mans/index_reads.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH INDEX_READS "1" "August 2020" "fast5-research" "User Commands"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">index_reads \- build index of reads within .fast5 files. Output to stdout.</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH DESCRIPTION</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">index_reads [\-h] [\-\-recursive] [\-\-workers WORKERS] input</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.SS "positional arguments:"</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">input</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.br</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\&.fast5 directory</span>
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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">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.SS "optional arguments:"</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">show this help message and exit</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-\-recursive\fR</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Search recursively under `input` for source files.</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-\-workers\fR WORKERS</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Number of worker processes.</span></pre>
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<li id="a9416cda73c67a0208d9eeba43adb840a3ba0017">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#a9416cda73c67a0208d9eeba43adb840a3ba0017"><strong>debian/mans/read_summary.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH READ_SUMMARY "1" "August 2020" "fast5-research" "User Commands"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">read_summary \- summarise reads stored in a bulk .fast5. </span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH DESCRIPTION</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">read_summary [\-h] [\-\-channel_range CHANNEL_RANGE CHANNEL_RANGE] input output</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.SS "positional arguments:"</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">input</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.br</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Bulk .fast5 file for input.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.TP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">output</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.br</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Output text file.</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SS "optional arguments:"</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
</pre>
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17
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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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18
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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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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-\-channel_range\fR CHANNEL_RANGE CHANNEL_RANGE</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Channel range (inclusive).</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/fast5-research/-/commit/d514d956031f678e5ad1d92240873ef4e47c8de0#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,6 @@ override_dh_auto_build: export https_proxy=127.0.0.1:9</td>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_auto_build:</span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_auto_build</span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> PYTHONPATH=. python3 -m sphinx -N -bhtml docs/ build/html # HTML generator</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> PYTHONPATH=. python3 -m sphinx -N -bman docs/ build/man # Manpage generator</span>
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20
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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21
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">override_dh_auto_test:</span>
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22
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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