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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/ivar">Debian Med / ivar</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/fa696fe8176e2c3eb37ea9d75bff2ff504a6b9ea">fa696fe8</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-16T21:54:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update debian/source/lintian-overrides
A change in the format of the detection of lines too long for a source
code is causing a mismatched-override lintian warning (in addition to
the error that cropped back up).
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/2324e5beae5e9d2a15c6381b255f8338e9fffaa7">2324e5be</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-16T22:04:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add privacy-breach.patch to point to local diagram
The diagram shown was initially pulled from github. Thanks lintian
for catching this!
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ivar/-/commit/f2c38ea22ac7797e28d770ff0c161967c1581db4">f2c38ea2</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-09-16T22:31:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ready to upload to unstable
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#7fab45fa1cc88bacd79ff99d4820ca45a30667fa">
<span class="new-file">
+
debian/patches/privacy-breach.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#85ccdeeb03055211183e48520592d9a93592b330">
debian/source/lintian-overrides
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/ivar/-/compare/f3c9011e6fab964049f86206fa9159ff80035f58...f2c38ea22ac7797e28d770ff0c161967c1581db4#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ivar (1.3.1+dfsg-2) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ivar (1.3.1+dfsg-2) <span class="idiff left right">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"> * add forward-build-options.patch; build ivar with <span class="idiff left right">Debian</span> build options</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * add forward-build-options.patch; build ivar with <span class="idiff left right">hardened</span> build options</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * add gcc-11.patch; fixes ftbfs with Gcc 11 (Closes: #984067)</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * d/salsa-ci.yml: allow reproducible build test to fail, for the moment</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * update d/s/lintian-overrides to match the new lintian semantics against the</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> false positive</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * add privacy-breach.patch to point to the local diagram in cookbook.html,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> instead of the github page</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="LC7" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> <span class="idiff left right">Sat, 28 Aug 2021 11:17:19</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> <span class="idiff left right">Thu, 16 Sep 2021 22:22:30</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">ivar (1.3.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/f3c9011e6fab964049f86206fa9159ff80035f58...f2c38ea22ac7797e28d770ff0c161967c1581db4#7fab45fa1cc88bacd79ff99d4820ca45a30667fa"><strong>debian/patches/privacy-breach.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: fix privacy-breach-generic in cookbookpage.html</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The document refers to a diagram hosted on github, but there is a local copy</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> readily available for use, so lets use this one.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> The file layout is somewhat odd, so I refrained to forward upstream.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="p">Author: Étienne Mollier <emollier@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">Last-Update: 2021-09-16</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- ivar.orig/docs/html/cookbookpage.html</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ ivar/docs/html/cookbookpage.html</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="p">@@ -73,7 +73,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> <p>The two pipelines are distributed along with iVar and are present in the<a href="https://github.com/andersen-lab/ivar/tree/master/pipeline">pipeline/</a> and <a href="https://github.com/andersen-lab/ivar/tree/master/pipeline_field">pipeline_field/</a> fodlers respectively.</p></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> <p>For both pipelines, there are four parameters that will have to be set in beginning of the Snakefile.</p></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> <div class="fragment"><div class="line">in_dir = "<input fastq files>"</div><div class="line">out_dir = "<output directory>"</div><div class="line">bed = "<bed-file-with-primer-positions>"</div><div class="line">ref="<path to reference fasta>"</div></div><!-- fragment --><div class="image"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-<img src="https://raw.githubusercontent.com/andersen-lab/ivar/master/pipeline/pipeline.png" width="500"/></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+<img src="./pipeline.png/pipeline.png" width="500"/></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </div></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> <h3>Call iSNVs from samples with known reference sequence</h3></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> <p><a href="https://github.com/andersen-lab/paper_2018_primalseq-ivar/blob/master/cookbook/CookBook.ipynb">Link to Jupyter Notebook</a></p></span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/f3c9011e6fab964049f86206fa9159ff80035f58...f2c38ea22ac7797e28d770ff0c161967c1581db4#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Fix-warning.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">forward-build-options.patch</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">gcc-11.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">privacy-breach.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ivar/-/compare/f3c9011e6fab964049f86206fa9159ff80035f58...f2c38ea22ac7797e28d770ff0c161967c1581db4#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># False positive</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">ivar source: source-is-missing docs/html/menu.js line length is 695 characters (>512)</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ivar source: source-is-missing docs/html/menu.js line 26 is 695 characters long (>512)</span></pre>
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