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<h3>
Sascha Steinbiss pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ariba">Debian Med / ariba</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2">3e10523f</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2020-05-21T19:18:17+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.14.5+ds</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#7a80c60d21d93a56bef168cf8344cea1c7c1212c">
ariba/megares_zip_parser.py
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<li class="file-stats">
<a href="#6167ac81f0b5f3ba99320e8a64262ff9453da115">
ariba/tasks/summary.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,7 @@ python:</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"><span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.6'</span></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">
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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="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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<td class="diff-line-num old_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="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="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install pysam</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" 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="diff-line-num new_line" data-linenumber="15" 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="LC15" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">source ./install_dependencies.sh</span></span>
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<td class="diff-line-num old_line" data-linenumber="15" 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="diff-line-num new_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">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"><span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></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">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install codecov</span></span>
</pre>
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<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Change Log</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="3" 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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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC3" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">v2.14.4</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/ariba/tree/v2.14.4</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="sx" style="color: #d14;"><span class="idiff right">2019-09-2</span>4</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="4" 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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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.<span class="idiff left right">3...v2.14.4</span></span><span class="p">)</span></span>
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<td class="diff-line-num new old_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="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="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">## [v2.14.5](https://github.com/sanger-pathogens/ariba/tree/v2.14.5) (2020-05-1</span>4)</span></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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.<span class="idiff left right">4...v2.14.5</span></span><span class="p">)</span></span>
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5
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<td class="diff-line-num new_line" data-linenumber="5" 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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="6" 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="LC6" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**<span class="idiff left right">Fixed bug</span>s:**</span></span>
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<td class="diff-line-num new old_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="LC6" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**<span class="idiff left right">Closed issue</span>s:**</span></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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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">-</span> Megares Downloading Error <span class="p">[</span><span class="nv" style="color: #008080;">\#294</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/294</span><span class="p">)</span></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="markdown"><span class="p">-</span> Summarising MLST reports? <span class="p">[</span><span class="nv" style="color: #008080;">\#292</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/292</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">-</span> CARD 3.0.6 introduces white space in seq id causing fasta/metadata mismatch <span class="p">[</span><span class="nv" style="color: #008080;">\#284</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/284</span><span class="p">)</span></span>
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8
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">-</span> ARGannot download fails <span class="p">[</span><span class="nv" style="color: #008080;">\#281</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/281</span><span class="p">)</span></span>
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9
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line old" 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="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">v2.14.3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/tree/v2.14.3</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">2019-08-23</span><span class="p">)</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">-</span> bump version number <span class="p">[</span><span class="nv" style="color: #008080;">\#297</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/297</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">-</span> Handle megares 2.0.0 <span class="p">[</span><span class="nv" style="color: #008080;">\#295</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/295</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[martinghunt](https://github.com/martinghunt</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">-</span> Correct swapped col and row filters <span class="p">[</span><span class="nv" style="color: #008080;">\#288</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/288</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[aunderwo](https://github.com/aunderwo</span><span class="p">)</span>)</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">-</span> Remove support information <span class="p">[</span><span class="nv" style="color: #008080;">\#286</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/286</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</span><span class="p">)</span>)</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.14.4](https://github.com/sanger-pathogens/ariba/tree/v2.14.4) (2019-09-24)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.3...v2.14.4</span><span class="p">)</span></span>
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22
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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 new new_line" data-linenumber="23" 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="LC23" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">-</span> Fixed GitHub issue <span class="se" style="color: #d14;">\#</span>281 - ARG-ANNOT Fails to Download <span class="p">[</span><span class="nv" style="color: #008080;">\#282</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/282</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</span><span class="p">)</span>)</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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="LC27" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.14.3](https://github.com/sanger-pathogens/ariba/tree/v2.14.3) (2019-08-30)</span></span>
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11
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<td class="diff-line-num new_line" data-linenumber="28" 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="LC28" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.2...v2.14.3</span><span class="p">)</span></span>
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12
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**<span class="idiff left right">Fixed bug</span>s:**</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**<span class="idiff left right">Closed issue</span>s:**</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">-</span> Version 3.0.3 of CARD breaks prepareref <span class="p">[</span><span class="nv" style="color: #008080;">\#278</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/278</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="p">-</span> RT 667288: Change docker file Ariba git clone to a copy</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">-</span> matplotlib listed twice as a dep in setup.py <span class="p">[</span><span class="nv" style="color: #008080;">\#275</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/275</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">-</span> v2.14.1 attributeError: 'Namespace' object has no attribute 'cdhit<span class="se" style="color: #d14;">\_</span>max<span class="se" style="color: #d14;">\_</span>memory' <span class="p">[</span><span class="nv" style="color: #008080;">\#273</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/273</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">-</span> Use ariba run for several isolates in batch <span class="p">[</span><span class="nv" style="color: #008080;">\#262</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/262</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">-</span> Stopping! Signal received: 13 <span class="p">[</span><span class="nv" style="color: #008080;">\#238</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/238</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="p">-</span> Added default locale to docker file <span class="p">[</span><span class="nv" style="color: #008080;">\#280</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/280</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">-</span> Fix for issue <span class="se" style="color: #d14;">\#</span>278 Version 3.0.3 of CARD breaks prepareref <span class="p">[</span><span class="nv" style="color: #008080;">\#279</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/279</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">-</span> Remove extra matplotlib entry in install<span class="se" style="color: #d14;">\_</span>requires <span class="p">[</span><span class="nv" style="color: #008080;">\#277</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/277</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andersgs](https://github.com/andersgs</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="p">-</span> Removed the specific Ariba release number from the docker file <span class="p">[</span><span class="nv" style="color: #008080;">\#276</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/276</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</span><span class="p">)</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="LC18" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">v2.14.2</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/ariba/tree/v2.14.2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="sx" style="color: #d14;"><span class="idiff right">2019-06-18</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">## [v2.14.2](https://github.com/sanger-pathogens/ariba/tree/v2.14.2) (2019-06-21</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.1...v2.14.2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="p">-</span> Added Spades assembler into Docker file - RT ticket 660940</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="p">-</span> Incremented release number</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"><span class="p">-</span> Added LICENSE file into release distribution - RT ticket 660890</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="p">-</span> Issue with ariba and slurm <span class="se" style="color: #d14;">\(</span>signal 18, signal 20<span class="se" style="color: #d14;">\)</span> <span class="p">[</span><span class="nv" style="color: #008080;">\#263</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/263</span><span class="p">)</span></span>
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26
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51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">v2.14.1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/tree/v2.14.1</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">2019-06-13</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="p">-</span> RT 660940 - add spades to docker file <span class="p">[</span><span class="nv" style="color: #008080;">\#274</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/274</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">-</span> Added AUTHORS and LICENSE to the manifest <span class="p">[</span><span class="nv" style="color: #008080;">\#272</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/272</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</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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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.14.1](https://github.com/sanger-pathogens/ariba/tree/v2.14.1) (2019-06-13)</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.14.0...v2.14.1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**<span class="idiff left right">Fixed bug</span>s:**</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**<span class="idiff left right">Merged pull request</span>s:**</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="p">-</span> Ariba fails to install from PyPI due to missing .h files in distribution. Related to MANIFEST.in change in <span class="p">[</span><span class="nv" style="color: #008080;">\#269</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/269</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"><span class="p">-</span> Fix for Issue <span class="p">[</span><span class="nv" style="color: #008080;">\#263</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/issues/263</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p">-</span> Backed out MANIFEST.in change. Bumped release number to v2.14.1. <span class="p">[</span><span class="nv" style="color: #008080;">\#271</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/pull/271</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[kpepper](https://github.com/kpepper</span><span class="p">)</span>)</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">v2.14.0</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/tree/v2.14.0</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">2019-06-06</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;"><span class="idiff left right">## </span>[v2.14.0](https://github.com/sanger-pathogens/ariba/tree/v2.14.0) (2019-06-06)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/compare/v2.13.5...v2.14.0</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></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">@@ -688,4 +717,4 @@</td>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="markdown"><span class="se" style="color: #d14;">\*</span> <span class="ge" style="font-style: italic;">*This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*</span></span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -4,6 +4,9 @@ Antimicrobial Resistance Identification By Assembly</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">For how to use ARIBA, please see the <span class="p">[</span><span class="nv" style="color: #008080;">ARIBA wiki page</span><span class="p">][</span><span class="ss" style="color: #990073;">ARIBA wiki</span><span class="p">]</span>.</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">PLEASE NOTE: we currently do not have the resources to provide support for Ariba - see the <span class="p">[</span><span class="nv" style="color: #008080;">Feedback/Issues</span><span class="p">](</span><span class="sx" style="color: #d14;">#feedbackissues</span><span class="p">)</span> section.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Unmaintained</span><span class="p">](</span><span class="sx" style="color: #d14;">http://unmaintained.tech/badge.svg</span><span class="p">)</span>](http://unmaintained.tech/) </span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/ariba.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/ariba) </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License: GPL v3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg</span><span class="p">)</span>](https://github.com/sanger-pathogens/ariba/blob/master/LICENSE) </span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000131-brightgreen.svg</span><span class="p">)</span>](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000131) </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">@@ -55,9 +58,12 @@ Summarise data from several runs:</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown">Please read the <span class="p">[</span><span class="nv" style="color: #008080;">ARIBA wiki page</span><span class="p">][</span><span class="ss" style="color: #990073;">ARIBA wiki</span><span class="p">]</span> for full usage instructions.</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Tutorials</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">The Jupyter notebook tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/pathogen-informatics-training</span><span class="p">)</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"></span>
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58
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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59
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug <span class="idiff left">please log it </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">here</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/ariba/issues</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> or email us at ariba-help@sanger.ac.uk</span>.</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown">If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug <span class="idiff left">you can log it </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">here</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/ariba/issues</span></span><span class="p"><span class="idiff right">)</span></span>.</span>
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61
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Required dependencies</span></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="69" 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="LC69" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Python3</span><span class="p">][</span><span class="ss" style="color: #990073;">python</span><span class="p">]</span> version >= 3.6.0</span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" 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="113" 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">@@ -107,7 +113,7 @@ To use ARIBA use a command like this (substituting in your directories), where y</td>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown">When calling Ariba via Docker (as above) you'll also need to add <span class="gs" style="font-weight: 600;">**/data/**</span> in front of all the passed in file or directory names (e.g. /data/my_output_folder).</span>
</pre>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="110" 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="LC110" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Debian (<span class="idiff left right">testing</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Debian (<span class="idiff left right">Ariba version may not be the latest</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown">ARIBA is available in the latest version of Debian, and over time will progressively filter through to Ubuntu and other distributions which use Debian. To install it as root:</span>
</pre>
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="113" 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="LC119" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sudo apt-get install ariba</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" 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="217" 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">@@ -211,7 +217,7 @@ Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions.</td>
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<td class="diff-line-num old_line" data-linenumber="211" 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="LC217" class="line" lang="markdown">ARIBA is free software, licensed under <span class="p">[</span><span class="nv" style="color: #008080;">GPLv3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/ariba/blob/master/LICENSE</span><span class="p">)</span>.</span>
</pre>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="213" 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="LC219" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Feedback/Issues</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="markdown"><span class="idiff left">Please report any issues to the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">issues page</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/ariba/issues</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> or email ariba-help@sanger.ac.uk</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"><span class="idiff left">We currently do not have the resources to provide support for Ariba. However, the community might be able to help you out if you report any issues about usage of the software to the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">issues page</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/sanger-pathogens/ariba/issues</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">.</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="markdown">If you use this software please cite:</span>
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<li id="7a80c60d21d93a56bef168cf8344cea1c7c1212c">
<a href="https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2#7a80c60d21d93a56bef168cf8344cea1c7c1212c"><strong>ariba/megares_zip_parser.py</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,8 +24,22 @@ class MegaresZipParser:</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Error making directory '</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">outdir</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Old <2.0.0 megares has eg these files:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_annotations_v1.01.csv</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_database_v1.01.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_to_external_header_mappings_v1.01.tsv</span></span>
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<td class="diff-line-num new new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares 2.0.0 has these files:</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_drugs_annotations_v2.00.csv</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_drugs_database_v2.00.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_modified_annotations_v2.00.csv</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_modified_database_v2.00.fasta</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># megares_to_external_header_mappings_v2.00.csv</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The sequences in *_modified_* files seem to be a superset of</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># *_drugs_*, so use the *_modified_* ones. This will happen</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># as long as we loop over sorted filenames, because the _modified_</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># csv and fasta are listed last</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">zfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">zipfile</span><span class="p">.</span><span class="n" style="color: #333;">ZipFile</span><span class="p">(</span><span class="n" style="color: #333;">zip_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">member</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">zfile</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">namelist</span></span><span class="p"><span class="idiff right">(</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">member</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">zfile</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">namelist</span></span><span class="p"><span class="idiff right">()</span>):</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'_annotations_'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">member</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">original_files</span><span class="p">[</span><span class="s" style="color: #d14;">'annotations'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">member</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="s" style="color: #d14;">'_database_'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">member</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">member</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.fasta'</span><span class="p">):</span></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">@@ -51,7 +65,7 @@ class MegaresZipParser:</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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53
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csv</span><span class="p">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">delimiter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">delimiter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">expected_columns</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">reader</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">fieldnames</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;"><span class="idiff left">not</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">expected_columns</span></span><span class="p"><span class="idiff">).</span></span><span class="n" style="color: #333;"><span class="idiff">issubset</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">set</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">reader</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">fieldnames</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">Error</span><span class="p">(</span><span class="s" style="color: #d14;">'Unexpected header in annotations file. Expected columns: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">expected_columns</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">' but got: '</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">reader</span><span class="p">.</span><span class="n" style="color: #333;">fieldnames</span><span class="p">))</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">reader</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="81" 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">@@ -67,7 +81,21 @@ class MegaresZipParser:</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_load_header_mappings_file</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">infile</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">MegaresZipParser</span><span class="p">.</span><span class="n" style="color: #333;">_csv_to_dict</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">'Source_Database'</span><span class="p">,</span> <span class="s" style="color: #d14;">'MEGARes_Header'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Source_Headers(space_separated)'</span><span class="p">},</span> <span class="s" style="color: #d14;">'MEGARes_Header'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Megares <2.0.0 uses a tsv file, whereas 2.0.0 uses csv.</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Also, the column names changed slightly for 2.0.0, so we'll change</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># them to be the same as <2.0.0 after loading the file</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">infile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".tsv"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">MegaresZipParser</span><span class="p">.</span><span class="n" style="color: #333;">_csv_to_dict</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">\</span><span class="se" style="color: #d14;">t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">'Source_Database'</span><span class="p">,</span> <span class="s" style="color: #d14;">'MEGARes_Header'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Source_Headers(space_separated)'</span><span class="p">},</span> <span class="s" style="color: #d14;">'MEGARes_Header'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">infile</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".csv"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MegaresZipParser</span><span class="p">.</span><span class="n" style="color: #333;">_csv_to_dict</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="s" style="color: #d14;">','</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">'Database'</span><span class="p">,</span> <span class="s" style="color: #d14;">'MEGARes_v2_header'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Source_header'</span><span class="p">},</span> <span class="s" style="color: #d14;">'MEGARes_v2_header'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">fixed_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">d</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">fixed_data</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="s" style="color: #d14;">"Source_Database"</span><span class="p">:</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"Database"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="s" style="color: #d14;">"Source_Headers(space_separated)"</span><span class="p">:</span> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"Source_header"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fixed_data</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<a href="https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2#6167ac81f0b5f3ba99320e8a64262ff9453da115"><strong>ariba/tasks/summary.py</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">@@ -64,8 +64,8 @@ def run(options):</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">outprefix</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">fofn</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">fofn</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">filenames</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">infiles</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">filter_rows</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">col</span>_filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'y'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">filter_columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">row</span>_filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'y'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">filter_rows</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">row</span>_filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'y'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">filter_columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left right">col</span>_filter</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'y'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">min_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">min_id</span><span class="p">,</span></span>
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70
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">cluster_cols</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">cluster_cols</span><span class="p">,</span></span>
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">make_phandango_tree</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">no_tree</span><span class="p">),</span></span>
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<a href="https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</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">@@ -55,7 +55,7 @@ vcfcall_mod = Extension(</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">minimap_mod</span><span class="p">,</span> <span class="n" style="color: #333;">fermilite_mod</span><span class="p">,</span> <span class="n" style="color: #333;">vcfcall_mod</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.14.<span class="idiff left right">4</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.14.<span class="idiff left right">5</span>'</span><span class="p">,</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'ARIBA: Antibiotic Resistance Identification By Assembly'</span><span class="p">,</span></span>
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'ariba'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'test_run_data/*'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tb_data/*'</span><span class="p">]},</span></span>
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