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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/nanolyse">Debian Med / nanolyse</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanolyse/-/commit/e715d8aed64036390a220edc833886ad4e755350">e715d8ae</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-24T18:17:27+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Get some rudimentary autopkgtest working
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/nanolyse/-/commit/25572efd5cd154ffc5912ae0ae8b4e7aa212605f">25572efd</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-24T18:18:44+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add FIXME
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/nanolyse/-/commit/0c01ca756817f05bf1ce45b4f5c813020fbc0c92">0c01ca75</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-24T18:20:34+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">cleanup after running
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<h4>5 changed files:</h4>
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<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
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+
debian/docs
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<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
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+
debian/examples
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<li class="file-stats">
<a href="#4d8bffeb70d7cbd4c77ded97a3a50b4af285e3e0">
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debian/tests/data/README
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<li class="file-stats">
<a href="#a3bbe6c290f408bbebfc0503f978cfafdb3498a8">
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debian/tests/data/paired_reads.fastq
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
<a href="https://salsa.debian.org/med-team/nanolyse/-/compare/e8eb16bedd156400e79ab24cadaf2176e6451f63...0c01ca756817f05bf1ce45b4f5c813020fbc0c92#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span></pre>
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<li id="9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
<a href="https://salsa.debian.org/med-team/nanolyse/-/compare/e8eb16bedd156400e79ab24cadaf2176e6451f63...0c01ca756817f05bf1ce45b4f5c813020fbc0c92#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/data/*</span></pre>
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<li id="4d8bffeb70d7cbd4c77ded97a3a50b4af285e3e0">
<a href="https://salsa.debian.org/med-team/nanolyse/-/compare/e8eb16bedd156400e79ab24cadaf2176e6451f63...0c01ca756817f05bf1ce45b4f5c813020fbc0c92#4d8bffeb70d7cbd4c77ded97a3a50b4af285e3e0"><strong>debian/tests/data/README</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">This fastq file was taken from package ncbi-blast+</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> c++/src/algo/blast/blastinput/unit_test/data/paired_reads.fastq</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">FIXME: I have no idea whether this data set makes any sense at all.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 15 May 2020 15:27:17 +0200</span></pre>
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<li id="a3bbe6c290f408bbebfc0503f978cfafdb3498a8">
<a href="https://salsa.debian.org/med-team/nanolyse/-/compare/e8eb16bedd156400e79ab24cadaf2176e6451f63...0c01ca756817f05bf1ce45b4f5c813020fbc0c92#a3bbe6c290f408bbebfc0503f978cfafdb3498a8"><strong>debian/tests/data/paired_reads.fastq</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@pair1 (both are read)</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GAATGTCCGTCTGGGTCTCCTTGTGCTGCGGTCCTGGCAACTCGTAGAATTTCTTACCAAAGTATCGATCCGGGAGATAGTACGATGGATACTCCGCCCTCAGCCTCTCG</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">+pair1</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">@pair2</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext">ATGTTTTCCGATCCCGCCCAGGAGTCGGTTGCCACGCAGACGGAGGCACAACCGGTTCCGTCGCCCATCTGCACCCCACTGCTGATGGTGGACGAGGATGGACGAAAGCG</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">+pair2</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">@incomplete1.1 (only the first is accepted)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">ATGTTTTCCGATCCCGCCCAGGAGTCGGTTGCCACGCAGACGGAGGCACAACCGGTTCCGTCGCCCATCTGCACCCCACTGCTGATGGTGGACGAGGATGGACGAAAGCG</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">+incomplete1.1</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">@incomplete1.2</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">+incomplete1.2</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFFF</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">@incomplete2.1 (only the second is accepted)</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">+incomplete2.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFFF</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">@incomplete2.2</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">ATGTTTTCCGATCCCGCCCAGGAGTCGGTTGCCACGCAGACGGAGGCACAACCGGTTCCGTCGCCCATCTGCACCCCACTGCTGATGGTGGACGAGGATGGACGAAAGCG</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">+incomplete2.2</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFBFFFF<FFFFFFFFFFFFFFFFBFFFFF<FFFFFFFFFFFFFFFFFFFFFFFF</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/nanolyse/-/compare/e8eb16bedd156400e79ab24cadaf2176e6451f63...0c01ca756817f05bf1ce45b4f5c813020fbc0c92#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">@@ -11,5 +11,4 @@ fi</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-c</span> /usr/share/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/reference/lambda.fasta.gz <span class="o" style="font-weight: 600;">></span> lambda.fasta</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>lambda.fasta | NanoLyse <span class="o" style="font-weight: 600;">></span> reads_without_lambda.fastq</span></pre>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>paired_reads.fastq | NanoLyse <span class="o" style="font-weight: 600;">></span> reads_without_lambda.fastq</span></pre>
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