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<h3>
Andreas Tille pushed to branch debian/jessie-backports-sloppy
at <a href="https://salsa.debian.org/med-team/kraken">Debian Med / kraken</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/7aadb7559d5264bfc577593a7bed71f92d0d75ed">7aadb755</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-07T12:44:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Slighly more robust method to obtain taxid of fasta files to at least enable reading the provided data examples of autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/d4d320a73ef49017fd0a2b1256036e50a6f2e2a2">d4d320a7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-07T12:59:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Forwarded issue upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/5b70f5b5d06090ed2b75ec079f44f98cfefae1e6">5b70f5b5</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-07T13:06:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/cfa81f03df30a4041e34bf4482fa49f49b844265">cfa81f03</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-07T13:18:13Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' into debian/jessie-backports-sloppy
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken/commit/5619acd2061ad6dc63e222d50cfd3f7c293455fd">5619acd2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-02-12T10:01:03Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to jessie-sloppy
</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#11795763e23b5c32505660a5130153553a1d8460">
<span class="new-file">
+
debian/patches/fix_reading_fasta.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kraken/compare/407ad4ca0d4e9983a53e07bacfbfec8196a47b2d...5619acd2061ad6dc63e222d50cfd3f7c293455fd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kraken (1.1-<span class="idiff left right">1</span>~bpo8+1) jessie-backports-sloppy; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">kraken (1.1-<span class="idiff left right">2</span>~bpo8+1) jessie-backports-sloppy; 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"> * Rebuild for jessie-backports-sloppy.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Revert to debhelper 10 (latest version in Jessie)</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"> -- Andreas Tille <tille@debian.org> Tue, 06 Feb 2018 14:44:02 +0100</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Mon, 12 Feb 2018 11:00:42 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">kraken (1.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Slighly more robust method to obtain taxid of fasta files to at least</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> enable reading the provided data examples of autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> Closes: #889623</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 07 Feb 2018 13:59:49 +0100</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">kraken (1.1-1) unstable; urgency=medium</span>
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<li id="11795763e23b5c32505660a5130153553a1d8460">
<a href="https://salsa.debian.org/med-team/kraken/compare/407ad4ca0d4e9983a53e07bacfbfec8196a47b2d...5619acd2061ad6dc63e222d50cfd3f7c293455fd#11795763e23b5c32505660a5130153553a1d8460"><strong>debian/patches/fix_reading_fasta.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Description: Slighly more robust method to obtain taxid of fasta files to at</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> least enable reading the provided data examples of autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Bug-Debian: https://bugs.debian.org/889623</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Forwarded: https://github.com/DerrickWood/kraken/issues/111</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Last-Update: Wed, 07 Feb 2018 13:41:39 +0100</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/scripts/scan_fasta_file.pl</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/scripts/scan_fasta_file.pl</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -32,6 +32,8 @@ while (<>) {</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> # while (/.../g) needed because non-redundant DBs sometimes have multiple</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> # sequence IDs in the header; extra sequence IDs are prefixed by</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> # '\x01' characters (if downloaded in FASTA format from NCBI FTP directly).</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s/^>gi\|/>/;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ s/\| .*//;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> while (/(?:^>|\x01)(\S+)/g) {</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> my $seqid = $1;</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> my $taxid = krakenlib::check_seqid($seqid);</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_jellyfish1.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">kraken_tmp_dir.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix_reading_fasta.patch</span></pre>
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