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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kaptive">Debian Med / kaptive</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/commit/63e43eb24c3c0649b811d3a72486dc5f1dcff1ce">63e43eb2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-24T15:48:38Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix lintian overrides
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/kaptive/commit/922f8837a6e4594835b35b7109dac282cb9d4469">922f8837</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-09-24T15:58:54Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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+
debian/createmanpages
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<li class="file-stats">
<a href="#b40d299721c0bfc2e4b34e0c751a83618eb5ddaa">
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+
debian/kaptive.py.1
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<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
debian/lintian-overrides
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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+
debian/manpages
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/kaptive/compare/d7285b1c4432f63dead18eafc361a2eeab597b4e...922f8837a6e4594835b35b7109dac282cb9d4469#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<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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<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="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">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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<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="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</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>.py</span>
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<pre style="margin: 0;">+<span id="LC16" 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="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC17" 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;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$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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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" 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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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></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;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" 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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<li id="b40d299721c0bfc2e4b34e0c751a83618eb5ddaa">
<a href="https://salsa.debian.org/med-team/kaptive/compare/d7285b1c4432f63dead18eafc361a2eeab597b4e...922f8837a6e4594835b35b7109dac282cb9d4469#b40d299721c0bfc2e4b34e0c751a83618eb5ddaa"><strong>debian/kaptive.py.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 1.47.11.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH KAPTIVE.PY "1" "September 2019" "kaptive.py 0.6.0" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">kaptive.py \- obtain information about K and O types for Klebsiella genome assemblies</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B kaptive.py</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\-h] [\-\-version] \fB\-a\fR ASSEMBLY [ASSEMBLY ...] \fB\-k\fR K_REFS</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">[\-g ALLELIC_TYPING] [\-o OUT] [\-v] [\-t THREADS]</span>
</pre>
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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">[\-\-no_seq_out] [\-\-no_table] [\-\-no_json]</span>
</pre>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">[\-\-start_end_margin START_END_MARGIN]</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">[\-\-min_gene_cov MIN_GENE_COV] [\-\-min_gene_id MIN_GENE_ID]</span>
</pre>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">[\-\-low_gene_id LOW_GENE_ID]</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">[\-\-min_assembly_piece MIN_ASSEMBLY_PIECE]</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">[\-\-gap_fill_size GAP_FILL_SIZE] [\-\-locus_label LOCUS_LABEL]</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.SH OPTIONS</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "optional arguments:"</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">show this help message and exit</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</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\-\-version\fR</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Show Kaptive's version number and exit</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-a\fR ASSEMBLY [ASSEMBLY ...], \fB\-\-assembly\fR ASSEMBLY [ASSEMBLY ...]</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">FASTA file(s) for assemblies (default: None)</span>
</pre>
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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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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">\fB\-k\fR K_REFS, \fB\-\-k_refs\fR K_REFS</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">GenBank file with reference loci (default: None)</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\-g\fR ALLELIC_TYPING, \fB\-\-allelic_typing\fR ALLELIC_TYPING</span>
</pre>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">SRST2\-formatted FASTA file of allelic typing genes to</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">include in results (default: None)</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.TP</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">\fB\-o\fR OUT, \fB\-\-out\fR OUT</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Output directory/prefix (default: ./kaptive_results)</span>
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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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-verbose\fR</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Display detailed information about each assembly in</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">stdout (default: False)</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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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS</span>
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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">The number of threads to use for the BLAST searches</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">(default: 4)</span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.TP</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-\-no_seq_out\fR</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Suppress output files of sequences matching locus</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">(default: False)</span>
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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\-\-no_table\fR</span>
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<td class="diff-line-num new new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Suppress output of tab\-delimited table (default:</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">False)</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.TP</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-\-no_json\fR</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Suppress output of JSON file (default: False)</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\-\-start_end_margin\fR START_END_MARGIN</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">Missing bases at the ends of locus allowed in a</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">perfect match. (default: 10)</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.TP</span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">\fB\-\-min_gene_cov\fR MIN_GENE_COV</span>
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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">minimum required % coverage for genes (default: 90.0)</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.TP</span>
</pre>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">\fB\-\-min_gene_id\fR MIN_GENE_ID</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">minimum required % identity for genes (default: 80.0)</span>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.TP</span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">\fB\-\-low_gene_id\fR LOW_GENE_ID</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">genes with a % identity below this value will be</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">flagged as low identity (default: 95.0)</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\-\-min_assembly_piece\fR MIN_ASSEMBLY_PIECE</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">minimum locus matching assembly piece to return</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">(default: 100)</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.TP</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">\fB\-\-gap_fill_size\fR GAP_FILL_SIZE</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">when separate parts of the assembly are found within</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">this distance, they will be merged (default: 100)</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\-\-locus_label\fR LOCUS_LABEL</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">In the Genbank file, the source feature must have a</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">note identifying the locus name, starting with this</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">label followed by a colon (e.g. /note="K locus: K1")</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">(default: automatically determined)</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">.SH AUTHOR</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">This manpage was written by Andreas Tille 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/kaptive/compare/d7285b1c4432f63dead18eafc361a2eeab597b4e...922f8837a6e4594835b35b7109dac282cb9d4469#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># see https://lists.debian.org/debian-med/2018/06/msg00043.html</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">#PKGNAME#</span>: script-with-language-extension usr/bin/*.*</span></pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">kaptive</span>: script-with-language-extension usr/bin/*.*</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/compare/d7285b1c4432f63dead18eafc361a2eeab597b4e...922f8837a6e4594835b35b7109dac282cb9d4469#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/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/kaptive/compare/d7285b1c4432f63dead18eafc361a2eeab597b4e...922f8837a6e4594835b35b7109dac282cb9d4469#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"></span>
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6
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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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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"></span>
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20
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">%:</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> dh $@</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#endif</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">override_dh_installman:</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh_installman --language=C</span></pre>
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