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GitLab

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<h3>

Andreas Tille pushed to branch master

at <a href="https://salsa.debian.org/med-team/pilon-non-free">Debian Med / pilon-non-free</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73">fb6a71cf</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-06-12T12:44:55+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging

</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

<span class="new-file">

+

debian/changelog

</span>

</a>

</li>

<li class="file-stats">

<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<span class="new-file">

+

debian/compat

</span>

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<span class="new-file">

+

debian/control

</span>

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<span class="new-file">

+

debian/copyright

</span>

</a>

</li>

<li class="file-stats">

<a href="#fc932f0eaa389a4e2b93916f3995aae4019ea823">

<span class="new-file">

+

debian/get-orig-source

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

<span class="new-file">

+

debian/rules

</span>

</a>

</li>

<li class="file-stats">

<a href="#53399f7f2dd7535c43cdcfa511a9c06044a9c238">

<span class="new-file">

+

debian/source/format

</span>

</a>

</li>

<li class="file-stats">

<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<span class="new-file">

+

debian/upstream/metadata

</span>

</a>

</li>

<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<span class="new-file">

+

debian/watch

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pilon-non-free (1.22-1) UNRELEASED; urgency=medium</span>

</pre>

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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="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Initial release (Closes: #<bug>)</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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5

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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>

</td>

</tr>

</table>

<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>

<hr>

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</td>

<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="plaintext">11</span></pre>

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</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: pilon-non-free</span>

</pre>

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2

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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>

</pre>

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3

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~),</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.1.4</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/pilon-non-free</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/pilon-non-free.git</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Homepage: https://github.com/broadinstitute/pilon/wiki</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Package: pilon-non-free</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Architecture: all</span>

</pre>

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14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Depends: ${misc:Depends},</span>

</pre>

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15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">         libhtsjdk-java</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Description: automated genome assembly improvement and variant detection tool</span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Pilon is a software tool which can be used to:</span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">  * Automatically improve draft assemblies</span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">  * Find variation among strains, including large event detection</span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> Pilon requires as input a FASTA file of the genome along with one or more</span>

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> BAM files of reads aligned to the input FASTA file. Pilon uses read</span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> alignment analysis to identify inconsistencies between the input genome and</span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> the evidence in the reads. It then attempts to make improvements to the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> input genome, including:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">  * Single base differences</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">  * Small indels</span>

</pre>

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27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">  * Larger indel or block substitution events</span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">  * Gap filling</span>

</pre>

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29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">  * Identification of local misassemblies, including optional opening</span>

</pre>

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30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">    of new gaps</span></pre>

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</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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>

</pre>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: pilon</span>

</pre>

</td>

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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Upstream-Contact: https://github.com/broadinstitute/pilon/issues</span>

</pre>

</td>

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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Source: https://github.com/broadinstitute/pilon/releases</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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Comment: The code is actually free but currently there is no method</span>

</pre>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">         to build</span>

</pre>

</td>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

</td>

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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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Files: *</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Copyright: Copyright 2012-2017 Broad Institute, Inc.</span>

</pre>

</td>

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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">License: GPL-2</span>

</pre>

</td>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>

</pre>

</td>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Files: debian/*</span>

</pre>

</td>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Copyright: 2018 Andreas Tille <tille@debian.org></span>

</pre>

</td>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">License: GPL-2</span>

</pre>

</td>

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>

</pre>

</td>

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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: GPL-2</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Pilon is free software: you can redistribute it and/or modify</span>

</pre>

</td>

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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"> it under the terms of the GNU General Public License version 2</span>

</pre>

</td>

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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"> as published by the Free Software Foundation.</span>

</pre>

</td>

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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"> .</span>

</pre>

</td>

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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"> Pilon is distributed in the hope that it will be useful,</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> GNU General Public License for more details.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> .</span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> On Debian systems you can find the full teyt of the GNU General</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> Public License at /usr/share/common-licenses/GPL-2.</span></pre>

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<br>

</li>

<li id="fc932f0eaa389a4e2b93916f3995aae4019ea823">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#fc932f0eaa389a4e2b93916f3995aae4019ea823"><strong>debian/get-orig-source</strong></a>

<hr>

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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="c" style="color: #998; font-style: italic;"># if you need to repack for whatever reason you can</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># use this script via uscan or directly</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># FIXME: currently the code is not conform to Debian Policy</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#        http://www.debian.org/doc/debian-policy/ch-source.html</span></span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#        "get-orig-source (optional)"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#        This target may be invoked in any directory, ...</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># --> currently it is assumed the script is called in the</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#     source directory featuring the debian/ dir</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Excluding files and repacking archives</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># --------------------------------------</span></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">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># See also mk-origtargz(1) and the --repack option to uscan(1), which</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># honor the Files-Excluded list in debian/copyright.</span></span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># That may be all you need, especially since the repack option can be set</span></span>

</pre>

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17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># in debian/watch.</span></span>

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For an example how to fetch source from sourceforge SVN see</span></span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#   https://anonscm.debian.org/git/debian-med/kmer-tools.git</span></span>

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>

</pre>

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22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nv" style="color: teal;">COMPRESS</span><span class="o" style="font-weight: 600;">=</span>xz</span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nv" style="color: teal;">NAME</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;">'/^Source/ { print $2 }'</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$@</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> upstream-version <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span><span class="nv" style="color: teal;">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="s1" style="color: #d14;">'s/\([0-9\.]\+\)-[0-9]\+$/\1/'</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell">    uscan <span class="nt" style="color: navy;">--force-download</span> <span class="nt" style="color: navy;">--no-symlink</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></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">

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="k" style="font-weight: 600;">    </span><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$@</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s?^.*--upstream-version </span><span class="se" style="color: #d14;">\(</span><span class="s2" style="color: #d14;">[0-9.]</span><span class="se" style="color: #d14;">\+\)</span><span class="s2" style="color: #d14;"> .*</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NAME</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.*?</span><span class="se" style="color: #d14;">\1</span><span class="s2" style="color: #d14;">?"</span><span class="sb" style="color: #d14;">`</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">    <span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-q</span> <span class="s2" style="color: #d14;">"upstream-version"</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></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="shell"><span class="k" style="font-weight: 600;">        </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Unable to parse version number"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

34

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell">        <span class="nb" style="color: #0086b3;">exit</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

35

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">    </span><span class="k" style="font-weight: 600;">fi</span></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="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

36

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

37

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nv" style="color: teal;">TARDIR</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">NAME</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span></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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> ../tarballs</span>

</pre>

</td>

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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="40" 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">

40

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../tarballs</span>

</pre>

</td>

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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># need to clean up the tarballs dir first because upstream tarball might</span></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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># contain a directory with unpredictable name</span></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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="k" style="font-weight: 600;">*</span></span>

</pre>

</td>

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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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TARDIR</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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</td>

<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="shell"><span class="nb" style="color: #0086b3;">mv</span> ../pilon-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span>.jar <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TARDIR</span><span class="k" style="font-weight: 600;">}</span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="46" 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">

46

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"></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="47" 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="LC47" class="line" lang="shell"><span class="nv" style="color: teal;">GZIP</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--best --no-name"</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">--owner</span><span class="o" style="font-weight: 600;">=</span>root <span class="nt" style="color: navy;">--group</span><span class="o" style="font-weight: 600;">=</span>root <span class="nt" style="color: navy;">--mode</span><span class="o" style="font-weight: 600;">=</span>a+rX <span class="nt" style="color: navy;">-caf</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$NAME</span><span class="s2" style="color: #d14;">"</span>_<span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span>.orig.tar.<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">COMPRESS</span><span class="k" style="font-weight: 600;">}</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TARDIR</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></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="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="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">TARDIR</span><span class="k" style="font-weight: 600;">}</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>

</pre>

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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="plaintext"></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># DH_VERBOSE := 1</span>

</pre>

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4

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">%:</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">      dh $@</span>

</pre>

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7

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">get-orig-source:</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">      . debian/get-orig-source</span></pre>

</td>

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<br>

</li>

<li id="53399f7f2dd7535c43cdcfa511a9c06044a9c238">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>

<hr>

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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="plaintext">3.0 (quilt)</span></pre>

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</table>

<br>

</li>

<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#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>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">  Author: ></span>

</pre>

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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>

</pre>

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4

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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>

</pre>

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5

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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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>

</pre>

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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>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  Journal: PLOSone</span>

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  Year: 2014</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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  Volume: 9</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  Number: 11</span>

</pre>

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11

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">  Pages: e11296</span>

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">  DOI: 10.1371/journal.pone.0112963</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">  PMID: 25409509</span>

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14

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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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15

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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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<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/pilon-non-free/commit/fb6a71cf0506c3325dc1ab5620b296b8ac21da73#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

<hr>

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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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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://github.com/broadinstitute/pilon/releases .*/download/v.*/pilon-(\d[\d.-]+)\.jar</span></pre>

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