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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/discosnp">Debian Med / discosnp</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/-/commit/c9253accfb6be207fe4c87e8afaea3ef7df500e2">c9253acc</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T16:58:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.6.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/-/commit/664dad23ca91d950b4301687503ff211a912ed52">664dad23</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-02-17T16:58:28+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/-/commit/102fa6b8290198a5147b40e851d6d4b40339a0c4">102fa6b8</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-02-17T16:58:32+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.6.2'
Update to upstream version '2.6.2'
with Debian dir 7410a55b12b471966c0fa13224c26928b2f2259e</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/-/commit/b71a55c3b045f3ec3c0d328ff430f435d6605517">b71a55c3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T16:58:40+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unnecessary Team Upload line in changelog.
Changes-By: lintian-brush
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/discosnp/-/commit/f77b965919257df8dd0a49677fa534c52343a48b">f77b9659</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-02-17T16:59:57+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
</pre>
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#f871d95d8d351f0be4a6af7861b646c368117e8a">
scripts/ClassVCF_creator.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/discosnp/-/compare/8732561a8097d9628b6a22ba497d1a1ca497d355...f77b965919257df8dd0a49677fa534c52343a48b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">discosnp (1:2.6.<span class="idiff left right">1-2) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">discosnp (1:2.6.<span class="idiff left right">2-1) unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right">* Team upload.</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> <span class="idiff left right">[ Étienne Mollier ]</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Adjust use_debian_packaged_gatb-core.patch to not include GatbCore</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Tue, 07 Dec 2021 22:38:17 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * New upstream version</span>
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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"> -- Andreas Tille <tille@debian.org> Thu, 17 Feb 2022 16:58:46 +0100</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">discosnp (1:2.6.1-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<li id="f871d95d8d351f0be4a6af7861b646c368117e8a">
<a href="https://salsa.debian.org/med-team/discosnp/-/compare/8732561a8097d9628b6a22ba497d1a1ca497d355...f77b965919257df8dd0a49677fa534c52343a48b#f871d95d8d351f0be4a6af7861b646c368117e8a"><strong>scripts/ClassVCF_creator.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1184" 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="1184" 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">@@ -1184,7 +1184,7 @@ class SNPSCLOSE(VARIANT):</td>
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1184
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<pre style="margin: 0;"> <span id="LC1184" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">variantID</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"_"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subIDs</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">])</span></span>
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1185
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1185
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<pre style="margin: 0;"> <span id="LC1185" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">][</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"."</span></span>
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1186
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<td class="new_line diff-line-num" data-linenumber="1186" 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">
1186
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<pre style="margin: 0;"> <span id="LC1186" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">][</span><span class="mi" style="color: #099;">6</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">filterField</span></span>
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1187
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<pre style="margin: 0;">-<span id="LC1187" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">][</span><span class="mi" style="color: #099;">7</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sa">f</span><span class="s" style="color: #d14;">"Ty</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">variantType</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;Rk=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rank</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;UL=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_unitig_left</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;UR=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_unitig_right</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;CL=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_contig_left</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;CR=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_contig_right</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;Genome=</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">nucleoRef</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;Sd=</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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1187
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<pre style="margin: 0;">+<span id="LC1187" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">][</span><span class="mi" style="color: #099;">7</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sa">f</span><span class="s" style="color: #d14;">"Ty<span class="idiff left right">=</span></span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">variantType</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;Rk=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rank</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;UL=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_unitig_left</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;UR=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_unitig_right</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;CL=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_contig_left</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;CR=</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">len_contig_right</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;Genome=</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">nucleoRef</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">;Sd=</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">reverse</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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1188
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1188
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<pre style="margin: 0;"> <span id="LC1188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">filterField</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"MULTIPLE"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">XA</span><span class="p">:</span></span>
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1189
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1189
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<pre style="margin: 0;"> <span id="LC1189" class="line" lang="python"> <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">][</span><span class="mi" style="color: #099;">7</span><span class="p">]</span><span class="o" style="font-weight: 600;">+=</span><span class="sa">f</span><span class="s" style="color: #d14;">";XA=</span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">VCFObject</span><span class="p">.</span><span class="n" style="color: #333;">XA</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">"</span></span>
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1190
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1190
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<pre style="margin: 0;"> <span id="LC1190" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#TODO: eviter ces "replace"</span></span>
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