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<h3>
Shayan Doust pushed to branch master
at <a href="https://salsa.debian.org/med-team/simka">Debian Med / simka</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/commit/039412903a63d69aca8298c46137b70591ad51a8">03941290</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-12T19:58:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Move binaries into /usr/bin
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/commit/b9b8d45964c86e9eef39a89b7f006ed431edbf9d">b9b8d459</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-12T20:11:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/commit/5f12ac25308bacffb57269840b904e59c2f6dc2d">5f12ac25</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-12T20:22:27Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix chrpath
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/simka/commit/5278db6eb8ebf95d88a6672de0f7b26a74946e75">5278db6e</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-09-12T20:28:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Replace back ${shlibs:Depends} for simka only
</pre>
</li>
</ul>
<h4>12 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#5e27554f09f5822d077c0d29a22bfe5889ec9fe6">
<span class="new-file">
+
debian/mans/simka.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#08ca51c540898d27e3c6ab303abe6333628b107c">
<span class="new-file">
+
debian/mans/simkaCount.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#ac4d53b57738b18415ecb6e6d5b878de179cf2ff">
<span class="new-file">
+
debian/mans/simkaCountProcess.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#dc6eecfbddaa102029b712208512b2dc93536d1c">
<span class="new-file">
+
debian/mans/simkaMerge.1
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</li>
<li class="file-stats">
<a href="#9462da3a4d6d0c16b5f2ec69d35c27fbf74c1d18">
<span class="new-file">
+
debian/mans/simkaMin.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#0e53440e7e6eb9c3b25a2dcfca40ea4422d3d5f3">
<span class="new-file">
+
debian/mans/simkaMinCore.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#90a569d3420f5c75f411e5d048a807ef7b2a306a">
<span class="new-file">
+
debian/mans/simkaMin_update.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#4e51b02d317852bd692ba7371056d109c8426b5f">
<span class="new-file">
+
debian/simka.install
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" 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="18" 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">@@ -18,7 +18,8 @@ Homepage: https://github.com/GATB/simka</td>
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<td class="diff-line-num old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line" data-linenumber="18" 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">
18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_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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<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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Package: simka</span>
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<td class="diff-line-num old_line" data-linenumber="20" 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">
20
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<td class="diff-line-num new_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<td class="diff-line-num old old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
21
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<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<td class="diff-line-num new old_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">
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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">Depends: ${shlibs:Depends},</span>
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<td class="diff-line-num new old_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">
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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">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> ${misc:Depends},</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> libgatbcore2</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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">
23
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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
24
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">Description: comparative metagenomics method dedicated to NGS datasets</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
24
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<td class="diff-line-num new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Simka is a de novo comparative metagenomics tool. Simka represents each</span>
</pre>
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<br>
</li>
<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian/mans</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<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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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<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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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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<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="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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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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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;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>simka</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" 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="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>simkaCount</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" 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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>simkaCountProcess</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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="LC28" 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="LC29" 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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>simkaMerge</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" 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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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>simkaMinCore</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" 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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41
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<pre style="margin: 0;">+<span id="LC41" 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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>simkaMin</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" 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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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>simkaMin_update</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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="LC52" 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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53
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<pre style="margin: 0;">+<span id="LC53" 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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC57" 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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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" 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="LC60" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#5e27554f09f5822d077c0d29a22bfe5889ec9fe6"><strong>debian/mans/simka.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 1.47.8.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SIMKA "1" "September 2019" "simka 1.5.1" "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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">simka \- comparative metagenomics method dedicated to NGS datasets</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">ERROR: Unknown parameter '\-h'</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ERROR: Option '\-in' is mandatory</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ERROR: Option '\-out\-tmp' is mandatory</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ERROR: Option '\-in' is mandatory</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.PP</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">[Simka options]</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-in\fR</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">(1 arg) : input file of samples. One sample per line: id1: filename1...</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-out\fR</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">(1 arg) : output directory for result files (distance matrices) [default './simka_results']</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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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-out\-tmp\fR</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">(1 arg) : output directory for temporary files</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">\fB\-keep\-tmp\fR</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">(0 arg) : keep temporary files</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-data\-info\fR (0 arg) :</span>
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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">compute (and display) information before running Simka, such as the number of reads per dataset</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-verbose\fR</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">(1 arg) : verbosity level [default '1']</span>
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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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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-version\fR</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">(0 arg) : version</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-help\fR</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">(0 arg) : help</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.IP</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">[distance options]</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.TP</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-simple\-dist\fR</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">(0 arg) : compute all simple distances (Chord, Hellinger...)</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\-complex\-dist\fR (0 arg) :</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">compute all complex distances (Jensen\-Shannon...)</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.IP</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">[kmer options]</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-kmer\-size\fR</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">(1 arg) : size of a kmer [default '21']</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.TP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">\fB\-abundance\-min\fR</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">(1 arg) : min abundance a kmer need to be considered [default '2']</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-abundance\-max\fR</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">(1 arg) : max abundance a kmer can have to be considered [default '999999999']</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-kmer\-shannon\-index\fR (1 arg) :</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">minimal Shannon index a kmer should have to be kept. Float in [0,2] [default '0']</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.IP</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">[read options]</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.TP</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">\fB\-max\-reads\fR</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">(1 arg) : maximum number of reads per sample to process. Can be \fB\-1\fR: use all reads. Can be 0: estimate it [default '\-1']</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.TP</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">\fB\-min\-read\-size\fR</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">(1 arg) : minimal size a read should have to be kept [default '0']</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.TP</span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">\fB\-min\-shannon\-index\fR (1 arg) :</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">minimal Shannon index a read should have to be kept. Float in [0,2] [default '0']</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.IP</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">[core options]</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.TP</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-nb\-cores\fR</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">(1 arg) : number of cores [default '0']</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">.TP</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">\fB\-max\-memory\fR (1 arg) :</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">max memory (MB) [default '5000']</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">.TP</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">\fB\-max\-count\fR</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">(1 arg) : maximum number of simultaneous counting jobs (a higher value improve execution time but increase temporary disk usage) [default '']</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">.TP</span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">\fB\-max\-merge\fR</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">(1 arg) : maximum number of simultaneous merging jobs (1 job = 1 core) [default '']</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.IP</span>
</pre>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">[cluster options]</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">.TP</span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">\fB\-count\-cmd\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">(1 arg) : command to submit counting job [default '']</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">.TP</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">\fB\-merge\-cmd\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">(1 arg) : command to submit merging job [default '']</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">.TP</span>
</pre>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">\fB\-count\-file\fR (1 arg) :</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">filename to the couting job template [default '']</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">.TP</span>
</pre>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">\fB\-merge\-file\fR (1 arg) :</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">filename to the merging job template [default '']</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.SH AUTHOR</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<br>
</li>
<li id="08ca51c540898d27e3c6ab303abe6333628b107c">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#08ca51c540898d27e3c6ab303abe6333628b107c"><strong>debian/mans/simkaCount.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 1.47.8.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SIMKACOUNT "1" "September 2019" "simkaCount 1.5.1" "User Commands"</span>
</pre>
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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">simkaCount \- comparative metagenomics method dedicated to NGS datasets</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
</pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ERROR: Unknown parameter '\-h'</span>
</pre>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ERROR: Option '\-out\-tmp\-simka' is mandatory</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ERROR: Option '\-bank\-name' is mandatory</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ERROR: Option '\-bank\-index' is mandatory</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">ERROR: Option '\-min\-read\-size' is mandatory</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">ERROR: Option '\-min\-shannon\-index' is mandatory</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ERROR: Option '\-max\-reads' is mandatory</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">ERROR: Option '\-nb\-datasets' is mandatory</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">ERROR: Option '\-nb\-partitions' is mandatory</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">ERROR: Option '\-in' is mandatory</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">.PP</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">[SimkaCount options]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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="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">\fB\-nb\-cores\fR</span>
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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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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">(1 arg) : number of cores [default '0']</span>
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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">.TP</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">\fB\-verbose\fR</span>
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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">(1 arg) : verbosity level [default '1']</span>
</pre>
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<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
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-version\fR</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">(0 arg) : version</span>
</pre>
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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">.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="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">\fB\-help\fR</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">(0 arg) : help</span>
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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="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">\fB\-out\-tmp\-simka\fR</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">(1 arg) : tmp output</span>
</pre>
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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="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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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-bank\-name\fR</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">(1 arg) : bank name</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" 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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-bank\-index\fR</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">(1 arg) : bank name</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.TP</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">\fB\-min\-read\-size\fR</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">(1 arg) : bank name</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-min\-shannon\-index\fR</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">(1 arg) : bank name</span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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\-max\-reads\fR</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">(1 arg) : bank name</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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\-nb\-datasets\fR</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">(1 arg) : bank name</span>
</pre>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">\fB\-nb\-partitions\fR</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">(1 arg) : bank name</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="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
</pre>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">\fB\-in\fR</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">(1 arg) : reads file</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
57
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<pre style="margin: 0;">+<span id="LC57" 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="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">\fB\-kmer\-size\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="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">(1 arg) : size of a kmer [default '31']</span>
</pre>
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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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<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="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">\fB\-abundance\-min\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">(1 arg) : min abundance threshold for solid kmers [default '0']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.TP</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">\fB\-abundance\-max\fR</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">(1 arg) : max abundance threshold for solid kmers [default '2147483647']</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.TP</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">\fB\-abundance\-min\-threshold\fR</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">(1 arg) : min abundance hard threshold (only used when min abundance is "auto") [default '2']</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.TP</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">\fB\-histo\-max\fR</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">(1 arg) : max number of values in kmers histogram [default '10000']</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\-solidity\-kind\fR</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">(1 arg) : way to compute counts of several files (sum, min, max, one, all, custom) [default 'sum']</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.TP</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">\fB\-solidity\-custom\fR</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">(1 arg) : when solidity\-kind is custom, specifies list of files where kmer must be present [default '']</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">.TP</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">\fB\-max\-memory\fR</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">(1 arg) : max memory (in MBytes) [default '5000']</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.TP</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">\fB\-max\-disk\fR</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">(1 arg) : max disk (in MBytes) [default '0']</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.TP</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">\fB\-solid\-kmers\-out\fR</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">(1 arg) : output file for solid kmers (only when constructing a graph) [default '']</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.TP</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">\fB\-out\fR</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">(1 arg) : output file [default '']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">\fB\-out\-dir\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">(1 arg) : output directory [default '.']</span>
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<td class="diff-line-num new new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">.TP</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">\fB\-out\-tmp\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="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">(1 arg) : output directory for temporary files [default '.']</span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" 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="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">\fB\-out\-compress\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">(1 arg) : h5 compression level (0:none, 9:best) [default '0']</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="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" 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="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">\fB\-storage\-type\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">(1 arg) : storage type of kmer counts ('hdf5' or 'file') [default 'hdf5']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
102
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<pre style="margin: 0;">+<span id="LC102" 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="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">\fB\-histo2D\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">(1 arg) : compute the 2D histogram (with first file = genome, remaining files = reads) [default '0']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" 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="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">\fB\-histo\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">(1 arg) : output the kmer abundance histogram [default '0']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">[kmer count, advanced performance tweaks options]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" 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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">\fB\-minimizer\-type\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">(1 arg) : minimizer type (0=lexi, 1=freq) [default '0']</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
113
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<pre style="margin: 0;">+<span id="LC113" 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="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">\fB\-minimizer\-size\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">(1 arg) : size of a minimizer [default '10']</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.TP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">\fB\-repartition\-type\fR (1 arg) :</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">minimizer repartition (0=unordered, 1=ordered) [default '0']</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="ac4d53b57738b18415ecb6e6d5b878de179cf2ff">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#ac4d53b57738b18415ecb6e6d5b878de179cf2ff"><strong>debian/mans/simkaCountProcess.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 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SIMKACOUNTPROCESS "1" "September 2019" "simkaCountProcess 1.5.1" "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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">simkaCountProcess \- comparative metagenomics method dedicated to NGS datasets</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">nohup: invalid option \fB\-\-\fR 'h'</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Try 'nohup \fB\-\-help\fR' for more information.</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">nohup: invalid option \fB\-\-\fR 'h'</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Try 'nohup \fB\-\-help\fR' for more information.</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">nohup: invalid option \fB\-\-\fR 'h'</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Try 'nohup \fB\-\-help\fR' for more information.</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">nohup: invalid option \fB\-\-\fR 'h'</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Try 'nohup \fB\-\-help\fR' for more information.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">nohup: invalid option \fB\-\-\fR 'h'</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Try 'nohup \fB\-\-help\fR' for more information.</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="dc6eecfbddaa102029b712208512b2dc93536d1c">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#dc6eecfbddaa102029b712208512b2dc93536d1c"><strong>debian/mans/simkaMerge.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 1.47.8.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SIMKAMERGE "1" "September 2019" "simkaMerge 1.5.1" "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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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">simkaMerge \- comparative metagenomics method dedicated to NGS datasets</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ERROR: Unknown parameter '\-h'</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="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">ERROR: Option '\-nb\-cores' is mandatory</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="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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ERROR: Option '\-kmer\-size' is mandatory</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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ERROR: Option '\-in' is mandatory</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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">ERROR: Option '\-out\-tmp\-simka' is mandatory</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">ERROR: Option '\-partition\-id' is mandatory</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ERROR: Option '\-nb\-cores' is mandatory</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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">ERROR: Option '\-max\-memory' is mandatory</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="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">ERROR: Option '\-kmer\-shannon\-index' is mandatory</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="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">.PP</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">[SimkaMerge options]</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">.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="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">\fB\-nb\-cores\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="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">(1 arg) : number of cores [default '0']</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="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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<pre style="margin: 0;">+<span id="LC20" 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="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\-verbose\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="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">(1 arg) : verbosity level [default '1']</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="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">.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">
</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
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-version\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">(0 arg) : version</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>
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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">\fB\-help\fR</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">(0 arg) : help</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\-nb\-cores\fR</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">(1 arg) : nb cores</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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<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\-kmer\-size\fR</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">(1 arg) : kmer size</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.TP</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">\fB\-in\fR</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">(1 arg) : input filename</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\-out\-tmp\-simka\fR</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">(1 arg) : tmp output</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\-partition\-id\fR</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">(1 arg) : bank name</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\-nb\-cores\fR</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">(1 arg) : bank name</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\-max\-memory\fR</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">(1 arg) : bank name</span>
</pre>
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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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<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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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-kmer\-shannon\-index\fR (1 arg) :</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">bank name</span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-simple\-dist\fR</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">(0 arg) : compute simple distances</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">\fB\-complex\-dist\fR</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">(0 arg) : compute complex distances</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="9462da3a4d6d0c16b5f2ec69d35c27fbf74c1d18">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#9462da3a4d6d0c16b5f2ec69d35c27fbf74c1d18"><strong>debian/mans/simkaMin.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 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SIMKAMIN "1" "September 2019" "simkaMin 1.5.1" "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">simkaMin \- comparative metagenomics method dedicated to NGS datasets</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">.SS "[main options]:"</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">\fB\-in\fR</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">(1 arg) : input file of datasets. One sample per line: id1: filename1...</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-out\fR</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">(1 arg) : output directory for result files (distance matrices) [Default: ./simka_results]</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-seed\fR</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">(1 arg) : seed used for random k\-mer selection [Default: 100]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-bin\fR</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">(1 arg) : path to simkaMinCore program (to be specified if not in PATH, or not in standard installation directory <simkaDir>/build/bin/simkaMinCore)</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.SS "[core options]:"</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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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\-nb\-cores\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">(1 arg) : number of cores [Default: 0]</span>
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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">.TP</span>
</pre>
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<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
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-max\-memory\fR</span>
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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">(1 arg) : max memory (MB) [Default: 8000]</span>
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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">.SS "[k-mer options]:"</span>
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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">.TP</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">\fB\-kmer\-size\fR</span>
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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">(1 arg) : size of a kmer [Default: 21]</span>
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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="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">\fB\-nb\-kmers\fR</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">(1 arg) : number of kmers used to compute distances [Default: 1000000]</span>
</pre>
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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="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">\fB\-filter\fR</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">(0 arg) : filter out k\-mer seen one time (potentially erroneous)</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.SS "[read options]:"</span>
</pre>
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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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<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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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-max\-reads\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">(1 arg) : maximum number of reads per sample to process [Default: 0]</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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<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="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-min\-read\-size\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">(1 arg) : minimal size a read should have to be kept [Default: 0]</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-min\-shannon\-index\fR</span>
</pre>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">(1 arg) : minimal Shannon index a read should have to be kept. Float in [0,2] [Default: 0]</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#0e53440e7e6eb9c3b25a2dcfca40ea4422d3d5f3"><strong>debian/mans/simkaMinCore.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 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SIMKAMINCORE "1" "September 2019" "simkaMinCore 1.5.1" "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">simkaMinCore \- comparative metagenomics method dedicated to NGS datasets</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">.B simkaMin</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,option\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[Distance computation options]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">sketch</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">: transform datasets in small sketches of k\-mers and their abundance</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">distance</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">: compute Jaccard and Bray\-Curtis distances between sketches</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">[Distance matrix manipulation options]</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">export</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">: export distance matrices stored in binary format</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">[Sketch options]</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">append</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">: merge multiple sketch files into a single one</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">info</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">: list datasets contained in a sketch file</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="90a569d3420f5c75f411e5d048a807ef7b2a306a">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#90a569d3420f5c75f411e5d048a807ef7b2a306a"><strong>debian/mans/simkaMin_update.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 1.47.8.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SIMKAMIN_UPDATE "1" "September 2019" "simkaMin_update 1.5.1" "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">simkaMin_update \- comparative metagenomics method dedicated to NGS datasets</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">.SS "[main options]:"</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.TP</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">\fB\-in\fR</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">(1 arg) : input file of datasets (datasets to add to existing simka results</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-in\-to\-update\fR</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">(1 arg) : path to existing simka results to update (existing results will be overwritten)</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-bin\fR</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">(1 arg) : path to simkaMinCore program (to be specified if not in PATH, or not in standard installation directory <simkaDir>/build/bin/simkaMinCore)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "[core options]:"</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-nb\-cores\fR</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">(1 arg) : number of cores [Default: 0]</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-max\-memory\fR</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">(1 arg) : max memory (MB) [Default: 8000]</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.SS "[k-mer options]:"</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-filter\fR</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">(0 arg) : filter out k\-mer seen one time (potentially erroneous)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.SS "[read options]:"</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-max\-reads\fR</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">(1 arg) : maximum number of reads per sample to process [Default: 0]</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">\fB\-min\-read\-size\fR</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">(1 arg) : minimal size a read should have to be kept [Default: 0]</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-min\-shannon\-index\fR</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">(1 arg) : minimal Shannon index a read should have to be kept. Float in [0,2] [Default: 0]</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/simka/compare/f4f86417d25ef53dc5a5cab094c6ea3d23f22a0f...5278db6eb8ebf95d88a6672de0f7b26a74946e75#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,8 +5,7 @@ export LC_ALL=C.UTF-8</td>
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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="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@ --with python3</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +14,7 @@ override_dh_install:</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> rm -r debian/tmp/usr/example \</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> debian/tmp/usr/scripts</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> chrpath --delete debian/<span class="idiff left right">tmp</span>/usr/bin/*</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> chrpath --delete debian/<span class="idiff left right">simka</span>/usr/bin/*</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> for file in debian/simkamin/usr/bin/*.py; do mv "$$file" "$${file%%.py}"; done</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> mv debian/simkamin/usr/bin/simkaMin_utils debian/simkamin/usr/bin/simkaMin_utils.py</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tmp</span><span class="o" style="font-weight: 600;">/</span><span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">bin</span></span></pre>
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