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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bio-rainbow">Debian Med / bio-rainbow</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/a22b2ef82be8857d0e5b95b9e5e4156fc3185b64">a22b2ef8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:41:33+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;"> * Enhance description
* cme fix dpkg-control
* Standards-Version: 4.1.4
* Point VCS fields to Salsa
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/b5d038fb3f854ee3804eb0663213306c94038ce1">b5d038fb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:49:00+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream source was repackaged to remove some files - do this with Files-Excluded instead of get-orig-source and express it with +dfsg prefix
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/210b7c06b112fcc3a783c4733b8c2753b4242622">210b7c06</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:49:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.0.4+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/f6ae07715ec5586572ae898d4f7303b8c6332a0e">f6ae0771</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:49:18+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.0.4+dfsg'
Update to upstream version '2.0.4+dfsg'
with Debian dir 5d5eb3b6290ce4f18a004a660ac402866fadcde3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/a8b362bbb6b89efda56c0f54e0728dc476168925">a8b362bb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:49:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 11
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/cb63fcfb74126dd20b314ae1df75f8e3d6c4d6b5">cb63fcfb</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:54:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Lintian override for script-with-language-extension
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/39991690cd96fd91a6fdf4917bec72bd999986e8">39991690</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:56:49+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/19479ac31d9e3edda06c0668be73fcb475bf8581">19479ac3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T14:58:14+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP5
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/a67cd2bd373e0b37812617cac584b5b85fb98fed">a67cd2bd</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T15:06:54+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">hardening+=all
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/f3d0b74b8a771ca2656aa0ee27c12f2a1f230ebf">f3d0b74b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T15:07:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Really fix copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/eda88020e0f07eea2738ba101f5751b16fb0eaf1">eda88020</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T15:08:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix description
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4c489f91ad92b9e7c1511e516d25c7fa7224711a">
<span class="deleted-file">
−
._Makefile
</span>
</a>
</li>
<li class="file-stats">
<a href="#9828f4d26a9a0c54ec6caf1a02556f700b601582">
<span class="deleted-file">
−
._tags
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#fc932f0eaa389a4e2b93916f3995aae4019ea823">
<span class="deleted-file">
−
debian/get-orig-source
</span>
</a>
</li>
<li class="file-stats">
<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">
<span class="new-file">
+
debian/lintian-overrides
</span>
</a>
</li>
<li class="file-stats">
<a href="#35e9f056c7219abca526eaf325c4f006a2a3cbfe">
debian/patches/rename_binary.patch
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="4c489f91ad92b9e7c1511e516d25c7fa7224711a">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#4c489f91ad92b9e7c1511e516d25c7fa7224711a"><strong>._Makefile</strong>
deleted
</a>
<hr>
No preview for this file type
<br>
</li>
<li id="9828f4d26a9a0c54ec6caf1a02556f700b601582">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#9828f4d26a9a0c54ec6caf1a02556f700b601582"><strong>._tags</strong>
deleted
</a>
<hr>
No preview for this file type
<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
<hr>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bio-rainbow (2.0.4<span class="idiff left right">-2) UNRELEASED; urgency=low</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bio-rainbow (2.0.4<span class="idiff left right">+dfsg-1) UNRELEASED; urgency=medium</span></span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
</pre>
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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"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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3
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Created debian/upstream/metadata</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * debian/control: updated standards-version to 4.1.0</span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Fri, 17 Nov 2017 23:51:08 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Enhance description</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * cme fix dpkg-control</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="plaintext"> * Standards-Version: 4.1.4</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Point VCS fields to Salsa</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> * Upstream source was repackaged to remove some files - do this with</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Files-Excluded instead of get-orig-source and express it with +dfsg prefix</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * debhelper 11</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Lintian override for script-with-language-extension</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * DEP3</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> * DEP5</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> * hardening=+all</span>
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20
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<pre style="margin: 0;">+<span id="LC20" 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"> -- Andreas Tille <tille@debian.org> Wed, 04 Jul 2018 14:39:26 +0200</span>
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7
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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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8
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">bio-rainbow (2.0.4-1) unstable; urgency=low</span>
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9
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">9</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"><span class="idiff left right">11</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">Source: bio-rainbow</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Section: science</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Priority: optional</span>
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4
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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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5
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Olivier Sallou <osallou@debian.org></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 9), help2man</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.1.0</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bio-rainbow.git</span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Vcs-Git: git://anonscm.debian.org/debian-med/bio-rainbow.git</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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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>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> help2man</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bio-rainbow</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bio-rainbow.git</span>
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10
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Homepage: http://sourceforge.net/projects/bio-rainbow/</span>
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11
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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12
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Package: bio-rainbow</span>
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13
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Architecture: any</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends}, ${misc:Depends}, perl</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> ${perl:Depends}</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Description: clustering and assembling short reads for bioinformatics</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> Efficient tool for clustering and assembling short reads, especially for RAD.</span></pre>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> Efficient tool for clustering and assembling short reads,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> especially for RAD.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> Rainbow is developed to provide an ultra-fast and memory-efficient</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> solution to clustering and assembling short reads produced by RAD-seq.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> First, Rainbow clusters reads using a spaced seed method. Then, Rainbow</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> implements a heterozygote calling like strategy to divide potential</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> groups into haplotypes in a top-down manner. long a guided tree, it</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> iteratively merges sibling leaves in a bottom-up manner if they are</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> similar enough. Here, the similarity is defined by comparing the 2nd</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> reads of a RAD segment. This approach tries to collapse heterozygote</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> while discriminate repetitive sequences. At last, Rainbow uses a greedy</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> algorithm to locally assemble merged reads into contigs. Rainbow not</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> only outputs the optimal but also suboptimal assembly results. Based on</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> simulation and a real guppy RAD-seq data, it is shown that Rainbow is</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> more competent than the other tools in dealing with RAD-seq data.</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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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: <span class="idiff left right">bio-r</span>ainbow</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Upstream-Name: <span class="idiff left right">R</span>ainbow</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: http://sourceforge.net/projects/bio-rainbow/</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Files-Excluded: */.*.*</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> */._*</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> */*.bak</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Copyright: 2003-2006, Li Heng <liheng@genomics.org.cn></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> 2003-2006, Heng Li <liheng@genomics.org.cn></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> 2011, Jue Ruan <ruanjue@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: GPL-3+</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">Files: stdaln.*</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Copyright: 2003-2006, Li Heng <liheng@genomics.org.cn></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,32 +27,11 @@ License: LGPL-2.1+</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> On Debian systems, the complete text of the GNU Lesser General</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> Public License version 2.1 can be found in "/usr/share/common-licenses/LGPL-2.1".</span>
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29
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">Copyright: 2003-2006, Li Heng <liheng@genomics.org.cn></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> 2003-2006, Heng Li <liheng@genomics.org.cn></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> 2011, Jue Ruan <ruanjue@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">License: GPL-3+</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> This package is free software; you can redistribute it and/or modify</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> the Free Software Foundation; either version 3 of the License, or</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> (at your option) any later version.</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> This package is distributed in the hope that it will be useful,</span>
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<pre style="margin: 0;">-<span id="LC33" 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="LC34" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext"> You should have received a copy of the GNU General Public License</span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> along with this program. If not, see <https://www.gnu.org/licenses/></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext"> .</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> On Debian systems, the complete text of the GNU General</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Copyright: 2015 Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">License: GPL-3+</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">License: GPL-3+</span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext"> This package is free software; you can redistribute it and/or modify</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> the Free Software Foundation; either version 2 of the License, or</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,8 +42,5 @@ License: GPL-3+</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext"> You should have received a copy of the GNU General Public License</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext"> along with this program. If not, see <https://www.gnu.org/licenses/></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> On Debian systems, the complete text of the GNU General</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> Public License version 3 can be found in "/usr/share/common-licenses/GPL-2".</span></pre>
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<li id="fc932f0eaa389a4e2b93916f3995aae4019ea823">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#fc932f0eaa389a4e2b93916f3995aae4019ea823"><strong>debian/get-orig-source</strong>
deleted
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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/bash</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-e</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="nv" style="color: teal;">PKG</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>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="nv" style="color: teal;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>uscan <span class="nt" style="color: navy;">--verbose</span> <span class="nt" style="color: navy;">--force-download</span> <span class="nt" style="color: navy;">--no-symlink</span> |</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"Newest version on remote site is .* local version is .*"</span> |</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: navy;">-n</span> 1 |</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">sed</span> <span class="s2" style="color: #d14;">"s/Newest version on remote site is </span><span class="se" style="color: #d14;">\(</span><span class="s2" style="color: #d14;">[a-z0-9.]</span><span class="se" style="color: #d14;">\+\)</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>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> ../tarballs</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ../tarballs</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nv" style="color: teal;">UTAR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"rainbow_</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">.tar.gz"</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv</span> ../<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">UTAR</span><span class="k" style="font-weight: 600;">}</span> <span class="nb" style="color: #0086b3;">.</span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xzf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">UTAR</span><span class="k" style="font-weight: 600;">}</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv </span>rainbow_<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span> <span class="nv" style="color: teal;">$PKG</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span>.orig</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;">cd</span> <span class="nv" style="color: teal;">$PKG</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span>.orig</span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> .<span class="k" style="font-weight: 600;">*</span>.c</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;">rm</span> .<span class="k" style="font-weight: 600;">*</span>.h</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> .<span class="k" style="font-weight: 600;">*</span>.pl</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> .<span class="k" style="font-weight: 600;">*</span>.bak</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">rm</span> .<span class="k" style="font-weight: 600;">*</span>.txt</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> ..</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="shell"></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="shell"><span class="nv" style="color: teal;">BZIP2</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"--best"</span> <span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-cjf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PKG</span><span class="k" style="font-weight: 600;">}</span>_<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span>.orig.tar.bz2 <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PKG</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span>.orig</span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: navy;">-rf</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PKG</span><span class="k" style="font-weight: 600;">}</span>-<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">VERSION</span><span class="k" style="font-weight: 600;">}</span>.orig</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">UTAR</span><span class="k" style="font-weight: 600;">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>
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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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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">bio-rainbow: script-with-language-extension usr/bin/*.pl</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#35e9f056c7219abca526eaf325c4f006a2a3cbfe"><strong>debian/patches/rename_binary.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Olivier Sallou</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: 2015-08-17 13:26:07 +0000</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: Avoid file name conflict with rainbow package and rename to bio-rainbow</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -16,9 +16,9 @@</span></span>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,8 +7,7 @@</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">DPKG_EXPORT_BUILDFLAGS = 1</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># see FEATURE AREAS in dpkg-buildflags(1)</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">#export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"># see ENVIRONMENT in dpkg-buildflags(1)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"># package maintainers to append CFLAGS</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,5 +24,3 @@ override_dh_installman:</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> help2man --no-discard-stderr ./bio-rainbow > bio-rainbow.1</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> dh_installman</span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span></pre>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">get-orig-source:</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"> debian/get-orig-source</span></pre>
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<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/70be3cbe5d563d429bf6657aa7ec80fef6fdb612...eda88020e0f07eea2738ba101f5751b16fb0eaf1#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=<span class="idiff left right">3</span></span>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=<span class="idiff left right">4</span></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">http://sf.net/bio-rainbow/rainbow_(\d\S*)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))</span></pre>
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3
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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"> http://sf.net/bio-rainbow/rainbow_(\d\S*)\.(?:zip|tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))</span></pre>
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