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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/unanimity">Debian Med / unanimity</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/unanimity/commit/e707cab2989b377de7e5c369a030bdab86459f6d">e707cab2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-24T10:39:12Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.3.0+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unanimity/commit/4d2777c0d44ea15b2c1091a8d9cdac50090b55c7">4d2777c0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-24T10:39:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/3.3.0+dfsg'
Update to upstream version '3.3.0+dfsg'
with Debian dir 4b1658e32c42081456b3079ebbf8416d73965b92</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unanimity/commit/291790798bd47480f6e664e750d011e7a817e0cd">29179079</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-24T10:39:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unanimity/commit/b4704009bcdbd9890802f7a7c9f40776433a153e">b4704009</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-24T10:39:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unanimity/commit/22f2bf244f460d6afc16cd853d7e70b5567cd3ff">22f2bf24</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-24T10:40:05Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/unanimity/commit/1be0803202feeba740dd461c1a250a2040575a59">1be08032</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-24T10:50:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
</a>
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/unanimity/compare/84620b81de797af1dd539723fd3914284e4a0abb...1be0803202feeba740dd461c1a250a2040575a59#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,21 +6,10 @@</td>
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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="markdown"></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="markdown"><span class="p">***</span></span>
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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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Availability</span></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">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="idiff left">The latest pre-release, developers-only linux binaries can be installed via </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: teal;"><span class="idiff">bioconda</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://bioconda.github.io/</span></span><span class="p"><span class="idiff right">)</span></span>.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="idiff left">Latest </span><span class="sb" style="color: #d14;"><span class="idiff">`ccs`</span></span><span class="idiff"> can be installed via bioconda package </span><span class="sb" style="color: #d14;"><span class="idiff right">`pbccs`</span></span>.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="sb" style="color: #d14;"> conda install pbccs</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="13" 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="LC13" class="line" lang="markdown">These binaries are not ISO compliant.</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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="LC14" class="line" lang="markdown">For research only.</span>
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<td class="diff-line-num old old_line" data-linenumber="15" 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="LC15" class="line" lang="markdown">Not for use in diagnostics procedures.</span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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="LC16" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" 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="LC17" class="line" lang="markdown">Official support is only provided for official and stable</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">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">SMRT Analysis builds</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.pacb.com/products-and-services/analytical-software/</span><span class="p">)</span></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">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown">provided by PacBio.</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">No support for source builds.</span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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="LC21" class="line" lang="markdown">No support via mail to developers.</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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="LC22" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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="LC23" class="line" lang="markdown">Binaries on bioconda are newer than GitHub source code.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">Please refer to our <span class="p">[</span><span class="nv" style="color: teal;">official pbbioconda page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/PacificBiosciences/pbbioconda</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">for information on Installation, Support, License, Copyright, and Disclaimer.</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [Circular Consensus Calling](doc/PBCCS.md)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></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">@@ -51,6 +40,17 @@ and place them in a subdirectory of `${SMRT_CHEMISTRY_BUNDLE_DIR}`:</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown">This will cause Unanimity to try to load models from all files in <span class="sb" style="color: #d14;">`${SMRT_CHEMISTRY_BUNDLE_DIR}/arrow`</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown">with a <span class="sb" style="color: #d14;">`.json`</span> suffix.</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Changelog</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p"> *</span> <span class="gs" style="font-weight: 600;">**3.3.0**</span>:</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="p"> *</span> Add a windowing approach to reduce computational complexity from quadratic to linear</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="p"> *</span> Improve multi-threading framework to increase throughput</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p"> *</span> Enhance XML output, propagate <span class="sb" style="color: #d14;">`CollectionMetadata`</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p"> *</span> Includes latest chemistry parameters</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="p"> *</span> 3.1.0:</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="p"> *</span> Add <span class="sb" style="color: #d14;">`--maxPoaCoverage`</span> to decrease runtime for unpolished output, special parameter for IsoSeq workflow</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p"> *</span> Chemistry parameters for SMRT Link v6.0</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"></span>
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54
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: teal;">PacBio open source license</span><span class="p">](</span><span class="sx" style="color: #d14;">LICENSE</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/unanimity/compare/84620b81de797af1dd539723fd3914284e4a0abb...1be0803202feeba740dd461c1a250a2040575a59#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">unanimity (3.3.0+dfsg-1) 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"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * debhelper 12</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.3.0</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 24 Jan 2019 11:40:05 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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1
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">unanimity (3.1.0+dfsg-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Initial release (Closes: #847310)</span>
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<a href="https://salsa.debian.org/med-team/unanimity/compare/84620b81de797af1dd539723fd3914284e4a0abb...1be0803202feeba740dd461c1a250a2040575a59#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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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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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">2</span></span></pre>
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<a href="https://salsa.debian.org/med-team/unanimity/compare/84620b81de797af1dd539723fd3914284e4a0abb...1be0803202feeba740dd461c1a250a2040575a59#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -5,7 +5,7 @@ Uploaders: Afif Elghraoui <afif@debian.org>,</td>
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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">Testsuite: autopkgtest-pkg-python</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">1</span>~),</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Build-Depends: debhelper (>= 1<span class="idiff left right">2</span>~),</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> cmake,</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> swig,</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">@@ -18,7 +18,7 @@ Build-Depends: debhelper (>= 11~),</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libpbcopper-dev,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libseqan2-dev,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> pandoc</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">2.1</span></span>
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<td class="diff-line-num new old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3.0</span></span>
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<td class="diff-line-num old_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/unanimity</span>
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<td class="diff-line-num old_line" data-linenumber="23" 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="LC23" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/unanimity.git</span>
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<td class="diff-line-num old_line" data-linenumber="24" 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="LC24" class="line" lang="plaintext">Homepage: https://github.com/PacificBiosciences/unanimity</span>
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