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<h3>
Stuart Prescott pushed to branch master
at <a href="https://salsa.debian.org/med-team/tvc">Debian Med / tvc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/tvc/-/commit/bc168444790383ec6603083195d468fdeb08918c">bc168444</a></strong>
<div>
<span>by Stuart Prescott</span>
<i>at 2020-03-01T16:07:31+11:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use Python 3 in package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tvc/-/commit/d9b250b73678613c6634c75556304d17b1cee335">d9b250b7</a></strong>
<div>
<span>by Stuart Prescott</span>
<i>at 2020-03-01T16:07:31+11:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update S-V to 4.5.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tvc/-/commit/e0c907d9f48841f7cbfe5e0c9367cf901258dfdb">e0c907d9</a></strong>
<div>
<span>by Stuart Prescott</span>
<i>at 2020-03-01T16:07:31+11:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Switch to debhelper-compat (= 12)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tvc/-/commit/634b53df55695e9733ce992c21e97208cdd26b57">634b53df</a></strong>
<div>
<span>by Stuart Prescott</span>
<i>at 2020-03-01T16:07:31+11:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add R3: no
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/tvc/-/commit/67c05a770495833ab9cc7dbaecc6e6f25e08df35">67c05a77</a></strong>
<div>
<span>by Stuart Prescott</span>
<i>at 2020-03-01T16:07:51+11:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add changelog for upload
</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
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−
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="#e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<span class="new-file">
+
debian/patches/python3.patch
</span>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">tvc (5.0.3+git20151221.80e144e+dfsg-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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<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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</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"> * Use Python 3 in scripts (Closes: #945720).</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add Rules-Requires-Root: no.</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Update Standards-Version to 4.5.0 (no changes required).</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"> * Switch to debhelper-compat (= 12).</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"> -- Stuart Prescott <stuart@debian.org> Sun, 01 Mar 2020 15:57:45 +1100</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">tvc (5.0.3+git20151221.80e144e+dfsg-2) unstable; urgency=medium</span>
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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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> [ Logan Rosen ]</span>
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<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
<a href="https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">11</span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="4" 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="diff-line-num unfold js-unfold new_line" data-linenumber="4" 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">@@ -4,23 +4,24 @@ Uploaders: Dominique Belhachemi <domibel@debian.org>,</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right"> (>= 11~</span>),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper<span class="idiff left right">-compat (= 12</span>),</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> cmake,</span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libbamtools-dev,</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libjsoncpp-dev,</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libarmadillo-dev,</span>
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<td class="diff-line-num old_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">
12
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libboost-math-dev,</span>
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13
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> libsmithwaterman-dev</span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">5.0</span></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/tvc</span>
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<td class="diff-line-num old_line" data-linenumber="16" 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">
16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/tvc.git</span>
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<td class="diff-line-num old_line" data-linenumber="17" 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">
17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Homepage: http://ioncommunity.thermofisher.com</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Rules-Requires-Root: no</span>
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18
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Package: tvc</span>
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20
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Architecture: any</span>
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21
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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22
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> ${misc:Depends},</span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> python</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python<span class="idiff left right">3</span></span>
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24
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Description: genetic variant caller for Ion Torrent sequencing platforms</span>
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<td class="diff-line-num old_line" data-linenumber="25" 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">
25
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> Torrent Variant Caller (TVC) is a genetic variant caller for</span>
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26
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> Ion Torrent sequencing platforms, and is specially optimized to exploit the</span>
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<li id="e246f69e945a7c2e9a8e25cfacfcac7714c92b69">
<a href="https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35#e246f69e945a7c2e9a8e25cfacfcac7714c92b69"><strong>debian/patches/python3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/variant_caller_pipeline.py</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/variant_caller_pipeline.py</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> # Copyright (C) 2011 Ion Torrent Systems, Inc. All Rights Reserved</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> import sys</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -12,7 +12,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> def printtime(message, *args):</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> if args:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> message = message % args</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "[ " + time.strftime('%a %Y-%m-%d %X %Z') + " ] " + message</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("[ " + time.strftime('%a %Y-%m-%d %X %Z') + " ] " + message)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> sys.stdout.flush()</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> sys.stderr.flush()</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="p">@@ -133,7 +133,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> json_file = open(options.paramfile, 'r')</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> parameters = json.load(json_file)</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> json_file.close()</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;">- if parameters.has_key('pluginconfig'):</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;">+ if 'pluginconfig' in parameters:</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> parameters = parameters['pluginconfig']</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> except:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> printtime('ERROR: No parameter file found at: ' + options.paramfile)</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/external/vcflib/multichoose/multipermute.py</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/external/vcflib/multichoose/multipermute.py</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> # multipermute.py - permutations of a multiset</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> # Erik Garrison <erik.garrison@bc.edu> 2010</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -92,7 +92,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> if multiset != []:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> for permutation in permutations(multiset):</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> for item in permutation:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print item,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print(item, end=" ")</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print()</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> else:</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- print "usage", sys.argv[0], "<multiset>"</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ print("usage", sys.argv[0], "<multiset>")</span></span></pre>
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<a href="https://salsa.debian.org/med-team/tvc/-/compare/5dcfc9d6151a421a74112f9f103e52d19aa5bb74...67c05a770495833ab9cc7dbaecc6e6f25e08df35#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -5,3 +5,4 @@ hurd.patch</td>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">sse.patch</span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">use_debian_packaged_smithwaterman.patch</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># use_debian_packaged_vcflib.patch</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">python3.patch</span></pre>
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