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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/genometester">Debian Med / genometester</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e">a304a40c</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-06-05T23:29:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest. Move manpages to d/man/
</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
</a>
</li>
<li class="file-stats">
<a href="#57912bd2440c649a983fee8251b93ba624bc9374">
debian/glistcompare.1
→
debian/man/glistcompare.1
</a>
</li>
<li class="file-stats">
<a href="#3cf52f066804e6e794ee5fff9bc65b175b3622c8">
debian/glistmaker.1
→
debian/man/glistmaker.1
</a>
</li>
<li class="file-stats">
<a href="#197d3909afc1fe38a0b2d9edad5c129024427b72">
debian/glistquery.1
→
debian/man/glistquery.1
</a>
</li>
<li class="file-stats">
<a href="#4d3af537faa7bc30b6266ed61edb68c77543ff85">
debian/gmer_caller.1
→
debian/man/gmer_caller.1
</a>
</li>
<li class="file-stats">
<a href="#17d775d406b55e2ab5722770d26237775a7a5d7e">
debian/gmer_counter.1
→
debian/man/gmer_counter.1
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
debian/manpages
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</li>
<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<span class="new-file">
+
debian/source/include-binaries
</span>
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
<li class="file-stats">
<a href="#5507459e3ed39ba08320b153d02ccd73399fe350">
<span class="new-file">
+
debian/tests/test-data/Ccr.fa.gz
</span>
</a>
</li>
<li class="file-stats">
<a href="#864c2e01c37ad3a67eed0f7971aaeea1b189944a">
<span class="new-file">
+
debian/tests/test-data/Mg.fa.gz
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="k" style="font-weight: 600;">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2" 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="LC2" class="line" lang="php"><span class="nx">________________________________________</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">execution</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="5" 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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
</pre>
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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="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="8" 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="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">genometester (4.0-1) UNRELEASED; urgency=medium</span>
</pre>
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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"> * Initial release (Closes: #900752)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add manpages</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add autopkgtest</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Mon, 04 Jun 2018 16:33:48 +0200</span></pre>
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<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</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">@@ -11,6 +11,20 @@ Files: debian/*</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: 2018 Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">License: GPL-3+</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Files: debian/tests/test-data/*</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Copyright: 2018 EMBL-EBI</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">License: unrestricted</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> EMBL-EBI itself places no additional restrictions on the use or redistribution</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> of the data available via its online services other than those provided by the</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> original data owners.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Comment: Ensembl Bacteria release 39</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> See http://bacteria.ensembl.org/Candidatus_carsonella_ruddii_dc/Info/Index</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> http://bacteria.ensembl.org/Mycoplasma_genitalium_g37/Info/Index</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> To download the files use:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> wget ftp://ftp.ensemblgenomes.org/pub/bacteria/release-39/fasta/bacteria_40_collection/candidatus_carsonella_ruddii_dc/dna/Candidatus_carsonella_ruddii_dc.ASM44157v1.dna.chromosome.Chromosome.fa.gz</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> wget ftp://ftp.ensemblgenomes.org/pub/bacteria/release-39/fasta/bacteria_13_collection/mycoplasma_genitalium_g37/dna/Mycoplasma_genitalium_g37.ASM2732v1.dna.chromosome.Chromosome.fa.gz</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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14
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">License: GPL-3+</span>
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15
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> This program is free software: you can redistribute it and/or modify</span>
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16
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</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">README.GenomeTester4.md</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">README.FastGT.md</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">debian/tests/test-data</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">debian/README.test</span></pre>
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<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#197d3909afc1fe38a0b2d9edad5c129024427b72"><strong>debian/glistquery.1</strong>
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<strong>debian/man/glistquery.1</strong>
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<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#17d775d406b55e2ab5722770d26237775a7a5d7e"><strong>debian/gmer_counter.1</strong>
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<strong>debian/man/gmer_counter.1</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">*.1</span></span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/<span class="idiff left right">man/*</span></span></pre>
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<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/test-data/Ccr.fa.gz</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/test-data/Mg.fa.gz</span></pre>
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<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span></pre>
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<a href="https://salsa.debian.org/med-team/genometester/commit/a304a40cdc895c51788629ec3e9d67ecd9a75a9e#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh -e</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nv" style="color: teal;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"genometester"</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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5
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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="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</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;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: navy;">-test</span>.XXXXXX<span class="k" style="font-weight: 600;">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test-data/<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="k" style="font-weight: 600;">*</span>.gz</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---glistmaker test---'</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell">/usr/bin/glistmaker Ccr.fa <span class="nt" style="color: navy;">-o</span> Ccr</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell">/usr/bin/glistmaker Mg.fa <span class="nt" style="color: navy;">-o</span> Mg</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---glistquery test---'</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell">/usr/bin/glistquery Ccr_16.list <span class="o" style="font-weight: 600;">></span> Ccr_16.query</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">/usr/bin/glistquery Mg_16.list <span class="o" style="font-weight: 600;">></span> Mg_16.query</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> Ccr_16.query <span class="o" style="font-weight: 600;">]</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> Mg_16.query <span class="o" style="font-weight: 600;">]</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---glistcompare test---'</span></span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">/usr/bin/glistcompare Ccr_16.list Mg_16.list <span class="nt" style="color: navy;">--union</span> <span class="nt" style="color: navy;">-o</span> Ccr_Mg</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell">/usr/bin/glistcompare Ccr_16.list Mg_16.list <span class="nt" style="color: navy;">--intersection</span> <span class="nt" style="color: navy;">-o</span> Ccr_Mg</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell">/usr/bin/glistcompare Ccr_16.list Mg_16.list <span class="nt" style="color: navy;">--difference</span> <span class="nt" style="color: navy;">-o</span> Ccr_Mg</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> Ccr_Mg_16_0_diff1.list <span class="o" style="font-weight: 600;">]</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> Ccr_Mg_16_intrsec.list <span class="o" style="font-weight: 600;">]</span></span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> Ccr_Mg_16_union.list <span class="o" style="font-weight: 600;">]</span></span></pre>
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