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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/libbio-coordinate-perl">Debian Med / libbio-coordinate-perl</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/commit/e9b32509354afd74cd39f9aa3da08da26dc170ab">e9b32509</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:57:17Z</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/libbio-coordinate-perl/commit/5982f0f0e715ac480a87dfa723ad010d49ceba97">5982f0f0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:58:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Point Vcs fields to salsa.debian.org
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/commit/9d6a488fa0aa22044ad3a8a33d674fa6070387f6">9d6a488f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T09:58:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.2.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/commit/2264ace2187e4b6c2af22f4f9fb510fbf7263e20">2264ace2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T10:08:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">s/Conflicts/Breaks/
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/commit/e09668e1d442fb3719ffd4330fa330ff304d7063">e09668e1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T11:07:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/commit/5f6162d56d2d2ee2cd6f8e5913296486174f4320">5f6162d5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-09-24T11:08:18Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
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+
debian/patches/series
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<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
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+
debian/patches/spelling.patch
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/compare/d2026642f8d05b291adc7a72b8a6a096ab5f9c86...5f6162d56d2d2ee2cd6f8e5913296486174f4320#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libbio-coordinate-perl (1.7.1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * debhelper 11</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * s/Conflicts/Breaks/</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Fix spelling</span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 24 Sep 2018 13:07:25 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext">libbio-coordinate-perl (1.7.1-2) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> * Team upload</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/compare/d2026642f8d05b291adc7a72b8a6a096ab5f9c86...5f6162d56d2d2ee2cd6f8e5913296486174f4320#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">1<span class="idiff left right">0</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/compare/d2026642f8d05b291adc7a72b8a6a096ab5f9c86...5f6162d56d2d2ee2cd6f8e5913296486174f4320#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,21 +2,22 @@ Source: libbio-coordinate-perl</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: perl</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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5
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6
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<pre style="margin: 0;"> <span id="LC6" 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 (>= 1<span class="idiff left right">0</span>)</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1~</span>)</span>
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7
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<td class="diff-line-num new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">Build-Depends-Indep: bioperl (>= 1.7.1),</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> perl</span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.0</span></span>
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10
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<td class="diff-line-num new_line old" 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">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">anonscm.debian.org/cgit/debian-med/libbio-coordinate-perl.git</span></span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">anonscm.debian.org/git/debian-med</span>/libbio-coordinate-perl.git</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> <span class="idiff left right"> </span>perl</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://<span class="idiff left right">salsa.debian.org/med-team/libbio-coordinate-perl</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Vcs-Git: https://<span class="idiff left right">salsa.debian.org/med-team</span>/libbio-coordinate-perl.git</span>
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12
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Homepage: https://metacpan.org/release/Bio-Coordinate</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Testsuite: autopkgtest-pkg-perl</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Package: libbio-coordinate-perl</span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Architecture: all</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Depends: ${perl:Depends}, ${misc:Depends},</span>
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<td class="diff-line-num old old_line" data-linenumber="18" 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">
18
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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> bioperl (>= 1.7.1)</span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Conflicts: bioperl (<= 1.7.0)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Depends: ${perl:Depends},</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ${misc:Depends},</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> bioperl (>= 1.7.1)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Breaks: bioperl (<= 1.7.0)</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Description: BioPerl modules for working with biological coordinates</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> The Bioperl project is a coordinated effort to collect computational methods</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> routinely used in bioinformatics into a set of standard CPAN-style,</span>
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<a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/compare/d2026642f8d05b291adc7a72b8a6a096ab5f9c86...5f6162d56d2d2ee2cd6f8e5913296486174f4320#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">spelling.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/libbio-coordinate-perl/compare/d2026642f8d05b291adc7a72b8a6a096ab5f9c86...5f6162d56d2d2ee2cd6f8e5913296486174f4320#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Fix spelling</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Last-Update: Mon, 24 Sep 2018 11:57:17 +0200</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/lib/Bio/Coordinate/Collection.pm</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/lib/Bio/Coordinate/Collection.pm</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;">@@ -367,7 +367,7 @@ are left to the calling code.</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> Title : _is_sorted</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> Usage : $newpos = $obj->_is_sorted;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Function: toggle for whether the (internal) coodinate mapper data are sorted</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Function: toggle for whether the (internal) coordinate mapper data are sorted</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> Example :</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> Returns : boolean</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> Args : boolean</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/Bio/Coordinate/ExtrapolatingPair.pm</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/Bio/Coordinate/ExtrapolatingPair.pm</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -180,7 +180,7 @@ can do that and set strict() to true.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> Function: Map the location from the input coordinate system</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> to a new value in the output coordinate system.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- In extrapolating coodinate system there is no location zero.</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ In extrapolating coordinate system there is no location zero.</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> Locations are...</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> Example :</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> Returns : new location in the output coordinate system or undef</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/lib/Bio/Coordinate/GeneMapper.pm</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/lib/Bio/Coordinate/GeneMapper.pm</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1004,7 +1004,7 @@ version 1.007001</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> =head1 DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> Bio::Coordinate::GeneMapper is a module for simplifying the mappings</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-of coodinate locations between various gene related locations in human</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+of coordinate locations between various gene related locations in human</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> genetics. It also adds a special human genetics twist to coordinate</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> systems by making it possible to disable the use of zero</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> (0). Locations before position one start from -1. See method</span></pre>
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