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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/xpore">Debian Med / xpore</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/xpore/-/commit/8259f050e3363733d79f368ccc1d06e96aa85a0c">8259f050</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-21T23:04:18+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add pyensmbl to Depends
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/xpore/-/commit/3e7bc643b98564b7c61cdcdfb2b9a18175945a4b">3e7bc643</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-21T17:37:17+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/xpore/-/commit/c2fb316202eae540f0e179db1cbad551d084b329">c2fb3162</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-21T18:00:24+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Minor change
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/xpore/-/commit/9ec450c06e840533e3fddedc928bea8864f98c4f">9ec450c0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-05-21T18:00:30+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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+
debian/createmanpages
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<li class="file-stats">
<a href="#9ee8090162bd4292b369545d4f2afcd52b232469">
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debian/xpore-dataprep.1
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<li class="file-stats">
<a href="#1ce11b45ce9e7ad85624eacd59b1d1ee5218be70">
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+
debian/xpore-diffmod.1
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<li class="file-stats">
<a href="#b9e837f0d17d2045ea78c000b0fa73e9d6fb5b4a">
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debian/xpore.manpages
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">xpore (1.0-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">xpore (1.0-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Steffen Moeller, Nilesh Patra ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Initial release (Closes:#988690)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> <span class="idiff left">Mon, 17</span> May 2021 <span class="idiff">18:57:10</span> +0<span class="idiff right">20</span>0</span></pre>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> <span class="idiff left">Fri, 21</span> May 2021 <span class="idiff">23:27:59</span> +0<span class="idiff right">53</span>0</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ Rules-Requires-Root: no</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Package: xpore</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">Depends: ${python3:Depends}, ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Depends: ${python3:Depends}, ${misc:Depends}<span class="idiff left right">, pyensembl</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Suggests: xpore-doc</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Description: Nanopore analysis of differential RNA modifications</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> RNA is transcribed from DNA, possibly spliced and exported to the</span>
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<a href="https://salsa.debian.org/med-team/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$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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<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>xpore-dataprep</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;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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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;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>xpore-diffmod</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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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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<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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/xpore.manpages</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" 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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<pre style="margin: 0;">+<span id="LC33" 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="LC34" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f#9ee8090162bd4292b369545d4f2afcd52b232469"><strong>debian/xpore-dataprep.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 XPORE-DATAPREP "1" "May 2021" "xpore-dataprep 1.0" "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">xpore-dataprep \- Nanopore analysis of differential RNA modifications</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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: xpore\-dataprep [\-h] \fB\-\-eventalign\fR EVENTALIGN \fB\-\-summary\fR SUMMARY \fB\-\-out_dir\fR</span>
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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">OUT_DIR [\-\-ensembl ENSEMBL] [\-\-species SPECIES]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[\-\-customised_genome] [\-\-reference_name REFERENCE_NAME]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-annotation_name ANNOTATION_NAME]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">[\-\-gtf_path_or_url GTF_PATH_OR_URL]</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">[\-\-transcript_fasta_paths_or_urls TRANSCRIPT_FASTA_PATHS_OR_URLS]</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">[\-\-skip_eventalign_indexing] [\-\-genome]</span>
</pre>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">[\-\-n_processes N_PROCESSES] [\-\-chunk_size CHUNK_SIZE]</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">[\-\-readcount_min READCOUNT_MIN]</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">[\-\-readcount_max READCOUNT_MAX] [\-\-resume]</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.SS "required arguments:"</span>
</pre>
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<td class="new_line diff-line-num new" 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">.TP</span>
</pre>
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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">\fB\-\-eventalign\fR EVENTALIGN</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">eventalign filepath, the output from nanopolish.</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">(default: None)</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-\-summary\fR SUMMARY</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">eventalign summary filepath, the output from</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">nanopolish. (default: None)</span>
</pre>
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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\-\-out_dir\fR OUT_DIR</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">output directory. (default: None)</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.SS "optional arguments:"</span>
</pre>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" 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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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">show this help message and exit</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="old_line diff-line-num new" 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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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-\-ensembl\fR ENSEMBL</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">ensembl version for gene\-transcript mapping. (default:</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">91)</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.TP</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-\-species\fR SPECIES</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">species for ensembl gene\-transcript mapping. (default:</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">homo_sapiens)</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\-\-customised_genome\fR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">if customised genome provided. (default: False)</span>
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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\-\-reference_name\fR REFERENCE_NAME</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">fasta reference name. (default: None)</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.TP</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-\-annotation_name\fR ANNOTATION_NAME</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">gtf annotation name. (default: None)</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.TP</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-\-gtf_path_or_url\fR GTF_PATH_OR_URL</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">gtf file path or url. (default: None)</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.TP</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-\-transcript_fasta_paths_or_urls\fR TRANSCRIPT_FASTA_PATHS_OR_URLS</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">transcript fasta paths or urls. (default: None)</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
</pre>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-\-skip_eventalign_indexing\fR</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">skip indexing the eventalign nanopolish output.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">(default: False)</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.TP</span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">\fB\-\-genome\fR</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">to run on Genomic coordinates. Without this argument,</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">the program will run on transcriptomic coordinates</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">(default: False)</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.TP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">\fB\-\-n_processes\fR N_PROCESSES</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">number of processes to run. (default: 1)</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">.TP</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">\fB\-\-chunk_size\fR CHUNK_SIZE</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">number of lines from nanopolish eventalign.txt for</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">processing. (default: 1000000)</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.TP</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">\fB\-\-readcount_min\fR READCOUNT_MIN</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">minimum read counts per gene. (default: 1)</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.TP</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">\fB\-\-readcount_max\fR READCOUNT_MAX</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">maximum read counts per gene. (default: 1000)</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.TP</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">\fB\-\-resume\fR</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">with this argument, the program will resume from the</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">previous run. (default: False)</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">.SH AUTHOR</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> This manpage was written by Nilesh Patra for the Debian distribution and</span>
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84
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<pre style="margin: 0;">+<span id="LC84" 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/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f#1ce11b45ce9e7ad85624eacd59b1d1ee5218be70"><strong>debian/xpore-diffmod.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 1.47.16.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH XPORE-DIFFMOD "1" "May 2021" "xpore-diffmod 1.0" "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">xpore-diffmod \- Nanopore analysis of differential RNA modifications</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: xpore\-diffmod [\-h] \fB\-\-config\fR CONFIG [\-\-n_processes N_PROCESSES]</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">[\-\-save_models] [\-\-resume] [\-\-ids [IDS ...]]</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS "required 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">\fB\-\-config\fR CONFIG</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">yaml configuraion filepath. (default: None)</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.SS "optional arguments:"</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">show this help message and exit</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-\-n_processes\fR N_PROCESSES</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">number of processes to run. (default: 1)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-\-save_models\fR</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">with this argument, the program will save the model</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">parameters for each id. (default: False)</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-\-resume\fR</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">with this argument, the program will resume from the</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">previous run. (default: False)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-\-ids\fR [IDS ...]</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">gene / transcript ids to model. (default: [])</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> This manpage was written by Nilesh Patra for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC33" 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/xpore/-/compare/766a3781d2b7117b8b14341e9009dbac54307910...9ec450c06e840533e3fddedc928bea8864f98c4f#b9e837f0d17d2045ea78c000b0fa73e9d6fb5b4a"><strong>debian/xpore.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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