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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kraken2">Debian Med / kraken2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken2/commit/b67a9ce0787713667efb2e0b52f01bb9721ddd97">b67a9ce0</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-14T12:57:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Take over fix from kraken which was not ported to kraken2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kraken2/commit/c7700aff600194683789ec75eaf970628834848a">c7700aff</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-03-14T13:03:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Deactivate parts of autopkgtest which are currently failing
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</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
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/kraken2/compare/31e5d8f6c1968f8a4ed56fa19c979d0206cf12b3...c7700aff600194683789ec75eaf970628834848a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,8 @@ Homepage: https://www.ccb.jhu.edu/software/kraken2/</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Package: kraken2</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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Architecture: any</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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> ncbi-blast+</span>
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<td class="diff-line-num new_line" data-linenumber="17" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Description: taxonomic classification system using exact k-mer matches</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> Kraken 2 is the newest version of Kraken, a taxonomic classification</span>
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<td class="diff-line-num new_line" data-linenumber="19" 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="LC19" class="line" lang="plaintext"> system using exact k-mer matches to achieve high accuracy and fast</span>
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<li id="11795763e23b5c32505660a5130153553a1d8460">
<a href="https://salsa.debian.org/med-team/kraken2/compare/31e5d8f6c1968f8a4ed56fa19c979d0206cf12b3...c7700aff600194683789ec75eaf970628834848a#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 $taxid = kraken2lib::check_seqid($seqid);</span></pre>
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<a href="https://salsa.debian.org/med-team/kraken2/compare/31e5d8f6c1968f8a4ed56fa19c979d0206cf12b3...c7700aff600194683789ec75eaf970628834848a#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fix_install.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">hardening+debug_options.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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<a href="https://salsa.debian.org/med-team/kraken2/compare/31e5d8f6c1968f8a4ed56fa19c979d0206cf12b3...c7700aff600194683789ec75eaf970628834848a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -4,9 +4,6 @@ pkg=kraken2</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: navy;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></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">@@ -17,7 +14,11 @@ gunzip -r *</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell">kraken2-build <span class="nt" style="color: navy;">--add-to-library</span> Acartia_tonsa.fasta <span class="nt" style="color: navy;">--db</span> test_db</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell">kraken2-build <span class="nt" style="color: navy;">--add-to-library</span> Acinetobacter_phage.fasta <span class="nt" style="color: navy;">--db</span> test_db</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell">kraken2-build <span class="nt" style="color: navy;">--build</span> <span class="nt" style="color: navy;">--minimizer-len</span> 5 <span class="nt" style="color: navy;">--db</span> test_db</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">kraken2 <span class="nt" style="color: navy;">--db</span> test_db test.fa <span class="o" style="font-weight: 600;">></span> kraken.output</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## kraken-report --db test_db kraken.output</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kraken2-build --build --minimizer-len 5 --db test_db</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This leads to</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## kraken2-build: number of minimizer spaces (6) exceeds max</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## for minimizer len (5); max: 1</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># kraken2 --db test_db test.fa > kraken.output</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># This leads to</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">## kraken2: database ("./test_db") does not contain necessary file taxo.k2d</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"></span></pre>
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