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<h3>
Sascha Steinbiss pushed to branch master
at <a href="https://salsa.debian.org/med-team/ariba">Debian Med / ariba</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/4d6c0399a7282ae89bd07bfe958b4359404c512e">4d6c0399</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2019-01-05T10:34:29Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.13.3+ds</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/7ae3300a985c92ac94646af1ead32d4ab06702dc">7ae3300a</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2019-01-05T10:34:39Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge tag 'upstream/2.13.3+ds'
Upstream version 2.13.3+ds
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ariba/commit/c19bd8301e626ae122eebb26be31c9d3d4cb64d9">c19bd830</a></strong>
<div>
<span>by Sascha Steinbiss</span>
<i>at 2019-01-05T10:35:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2a1e1b6414ed603b06fec0cdbe3def87a6de5920">
ariba/tb.py
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</li>
<li class="file-stats">
<a href="#2ddf549e659e1d1996ed53848d99db2802ba95a6">
<span class="new-file">
+
ariba/tb_data/panel.20190102.json
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</a>
</li>
<li class="file-stats">
<a href="#d1d8decdef34324978ce42ec5dfebc152f6885dd">
<span class="new-file">
+
ariba/tb_data/panel.20190102.txt
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</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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</ul>
<h4>Changes:</h4>
<li id="2a1e1b6414ed603b06fec0cdbe3def87a6de5920">
<a href="https://salsa.debian.org/med-team/ariba/compare/9e9d96b594f4a2a85f82cc3f0e82fea52fde1e99...c19bd8301e626ae122eebb26be31c9d3d4cb64d9#2a1e1b6414ed603b06fec0cdbe3def87a6de5920"><strong>ariba/tb.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="212" 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">@@ -212,8 +212,8 @@ def write_prepareref_metadata_file(mutations, outfile):</td>
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<td class="diff-line-num old_line" data-linenumber="212" 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="LC212" class="line" lang="python"></span>
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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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<td class="diff-line-num new_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="LC213" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_prepareref_files</span><span class="p">(</span><span class="n" style="color: #333;">outprefix</span><span class="p">):</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="214" 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="214" 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="LC214" class="line" lang="python"> <span class="n" style="color: #333;">genbank_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'NC_000962.3.gb'</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="215" 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">
215
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<td class="diff-line-num new_line old" data-linenumber="215" 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="LC215" class="line" lang="python"> <span class="n" style="color: #333;">mut_to_drug_json</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.201<span class="idiff left right">81221</span>.json'</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="216" 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">
216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">panel_txt_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.201<span class="idiff left right">81221</span>.txt'</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="217" 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="215" 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="LC215" class="line" lang="python"> <span class="n" style="color: #333;">mut_to_drug_json</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.201<span class="idiff left right">90102</span>.json'</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="217" 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="216" 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="LC216" class="line" lang="python"> <span class="n" style="color: #333;">panel_txt_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">data_dir</span><span class="p">,</span> <span class="s" style="color: #d14;">'panel.201<span class="idiff left right">90102</span>.txt'</span><span class="p">)</span></span>
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<td class="diff-line-num old_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">
217
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<td class="diff-line-num 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">
217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="n" style="color: #333;">fasta_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.fa'</span></span>
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<td class="diff-line-num old_line" data-linenumber="218" 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">
218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">tsv_out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outprefix</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'.tsv'</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>
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<li id="2ddf549e659e1d1996ed53848d99db2802ba95a6">
<a href="https://salsa.debian.org/med-team/ariba/compare/9e9d96b594f4a2a85f82cc3f0e82fea52fde1e99...c19bd8301e626ae122eebb26be31c9d3d4cb64d9#2ddf549e659e1d1996ed53848d99db2802ba95a6"><strong>ariba/tb_data/panel.20190102.json</strong></a>
The diff for this file was not included because it is too large.
<br>
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<li id="d1d8decdef34324978ce42ec5dfebc152f6885dd">
<a href="https://salsa.debian.org/med-team/ariba/compare/9e9d96b594f4a2a85f82cc3f0e82fea52fde1e99...c19bd8301e626ae122eebb26be31c9d3d4cb64d9#d1d8decdef34324978ce42ec5dfebc152f6885dd"><strong>ariba/tb_data/panel.20190102.txt</strong></a>
The diff for this file was not included because it is too large.
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ariba/compare/9e9d96b594f4a2a85f82cc3f0e82fea52fde1e99...c19bd8301e626ae122eebb26be31c9d3d4cb64d9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ariba (2.13.3+ds-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * New upstream release.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Sascha Steinbiss <satta@debian.org> Sat, 05 Jan 2019 10:34:41 +0000</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">ariba (2.13.2+ds-1) unstable; urgency=medium</span>
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2
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> * New upstream release.</span>
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<a href="https://salsa.debian.org/med-team/ariba/compare/9e9d96b594f4a2a85f82cc3f0e82fea52fde1e99...c19bd8301e626ae122eebb26be31c9d3d4cb64d9#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;">'2.13.<span class="idiff left right">2</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;">'2.13.<span class="idiff left right">3</span>'</span><span class="p">,</span></span>
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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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<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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<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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