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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pilon">Debian Med / pilon</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon/commit/f40fb01e0da03b665697b46783b2cfd9059e2530">f40fb01e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-25T12:28:55+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging
</pre>
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<strong><a href="https://salsa.debian.org/med-team/pilon/commit/2638288bddefd3b3ff6a2579a7a98495d701b23e">2638288b</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-05-25T12:32:30+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends: libhtsjdk-java
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<h4>8 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
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debian/changelog
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<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
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debian/compat
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debian/control
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debian/copyright
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debian/rules
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debian/source/format
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debian/upstream/metadata
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debian/watch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pilon (1.22+dfsg-1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 23 Feb 2017 16:48:18 +0100</span></pre>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: pilon</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> scala,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> libscala-pickling-java</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pilon</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pilon.git</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Homepage: https://github.com/broadinstitute/pilon/wiki</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Package: pilon</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> libhtsjdk-java</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Description: automated genome assembly improvement and variant detection tool</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Pilon is a software tool which can be used to:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Automatically improve draft assemblies</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> * Find variation among strains, including large event detection</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Pilon requires as input a FASTA file of the genome along with one or more</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> BAM files of reads aligned to the input FASTA file. Pilon uses read</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> alignment analysis to identify inconsistencies between the input genome and</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> the evidence in the reads. It then attempts to make improvements to the</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> input genome, including:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> * Single base differences</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> * Small indels</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> * Larger indel or block substitution events</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> * Gap filling</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> * Identification of local misassemblies, including optional opening</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> of new gaps</span></pre>
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</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: pilon</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Upstream-Contact: https://github.com/broadinstitute/pilon/issues</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Source: https://github.com/broadinstitute/pilon/releases</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files-Excluded: lib/*</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Files: *</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Copyright: Copyright 2012-2017 Broad Institute, Inc.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">License: GPL-2</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Files: debian/*</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Copyright: 2018 Andreas Tille <tille@debian.org></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: GPL-2</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">License: GPL-2</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Pilon is free software: you can redistribute it and/or modify</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> it under the terms of the GNU General Public License version 2</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> as published by the Free Software Foundation.</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="LC20" class="line" lang="plaintext"> Pilon is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> On Debian systems you can find the full teyt of the GNU General</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Public License at /usr/share/common-licenses/GPL-2.</span></pre>
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</li>
<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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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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<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">%:</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> dh $@</span></pre>
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<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>
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<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: ></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Bruce J. Walker and Thomas Abeel and Terrance Shea and Margaret Priest</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> and Amr Abouelliel and Sharadha Sakthikumar and Christina A. Cuomo and</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Qiandong Zeng and Jennifer Wortman and Sarah K. Young and Ashlee M. Earl</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Title: "Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement"</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Journal: PLOSone</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Year: 2014</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> Volume: 9</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> Number: 11</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> Pages: e11296</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> DOI: 10.1371/journal.pone.0112963</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> PMID: 25409509</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0112963</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> eprint: http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0112963&type=printable</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/pilon/compare/b87dd34c21a685e1384babb52a3474e8a1a0d2ba...2638288bddefd3b3ff6a2579a7a98495d701b23e#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/broadinstitute/pilon/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)</span></pre>
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