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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/kmer">Debian Med / kmer</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmer/commit/7f2c720d37492eef4d105e5f7b141e03a93b0beb">7f2c720d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-27T14:50:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Provide test data in new package kmer-examples to avoid duplication of data in two packages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/kmer/commit/1dc82e0f62c19816f72ab2e3f62d4efd160f756d">1dc82e0f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-27T14:50:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#88d4677a2dd536c06ffb5ad9c65c0044a3cfc26c">
debian/atac.docs
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
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<li class="file-stats">
<a href="#e8db7227a188eedebdce52697849829e703cb187">
<span class="new-file">
+
debian/kmer-examples.README.Debian
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</li>
<li class="file-stats">
<a href="#90b669d683dd3181cfb62aeef460d13896f7ff28">
<span class="new-file">
+
debian/kmer-examples.docs
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</a>
</li>
<li class="file-stats">
<a href="#f83de6c204fa5f0197ff393cb6b4dd851dc482d7">
debian/sim4db.docs
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<li class="file-stats">
<a href="#8bead32e7e58d25ada9d9a6c43de1bfd8d7b4058">
debian/tests/atac-unit-test
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<li class="file-stats">
<a href="#250298e80304390409b063185886417f177a00db">
debian/tests/sim4db-unit-test
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<h4>Changes:</h4>
<li id="88d4677a2dd536c06ffb5ad9c65c0044a3cfc26c">
<a href="https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d#88d4677a2dd536c06ffb5ad9c65c0044a3cfc26c"><strong>debian/atac.docs</strong></a>
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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="LC1" class="line" lang="plaintext">README.atac</span>
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2
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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="LC2" class="line" lang="plaintext">debian/tests/atac-unit-test</span>
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">debian/tests/test-data/test_data.tar.gz</span>
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<td class="diff-line-num old_line" data-linenumber="4" 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="diff-line-num new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext">debian/README.test</span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">kmer (0~20150903+r2013-6) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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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="plaintext">kmer (0~20150903+r2013-6) <span class="idiff left right">unstable</span>; urgency=medium</span>
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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="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [ Liubov Chuprikova ]</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="6" 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="LC6" class="line" lang="plaintext"> * Add autopkgtest.</span>
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<td class="diff-line-num old_line" data-linenumber="5" 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="diff-line-num new_line" data-linenumber="7" 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="LC7" class="line" lang="plaintext"> * Standards-Version: 4.2.1</span>
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<td class="diff-line-num old_line" data-linenumber="6" 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="diff-line-num new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> * Add a patch to fix wrong evaluation order in an expression</span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> Closes: #906980</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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="diff-line-num new_line" data-linenumber="10" 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="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new old_line" data-linenumber="9" 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="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> * Provide test data in new package kmer-examples to avoid duplication of</span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"> data in two packages</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> -- Liubov Chuprikova <chuprikovalv@gmail.com> Mon, 27 Aug 2018 11:37:43 +0200</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">kmer (0~20150903+r2013-5) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -93,7 +93,8 @@ Package: sim4db</td>
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="plaintext">Recommends: leaff</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">Recommends: leaff,</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> kmer-examples</span>
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97
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">Description: batch spliced alignment of cDNA sequences to a target genome</span>
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98
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext"> Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="124" 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="diff-line-num unfold js-unfold new_line" data-linenumber="125" 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">@@ -124,6 +125,7 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext"> leaff,</span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext"> meryl,</span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"> gnuplot</span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">Recommends: kmer-examples</span>
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<td class="diff-line-num old_line" data-linenumber="127" 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="LC129" class="line" lang="plaintext">Description: genome assembly-to-assembly comparison</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext"> atac computes a one-to-one pairwise alignment of large DNA sequences. It first</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"> finds the unique k-mers in each sequence, chains them to larger blocks, and</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="140" 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="diff-line-num unfold js-unfold new_line" data-linenumber="142" 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">@@ -140,3 +142,17 @@ Description: genome assembly-to-assembly comparison</td>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext"> speed a comparisons of multiple sequences.</span>
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<td class="diff-line-num old_line" data-linenumber="141" 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="LC143" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="plaintext"> This package is part of the Kmer suite.</span>
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<td class="diff-line-num new new_line" data-linenumber="145" 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="LC145" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="146" 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="LC146" class="line" lang="plaintext">Package: kmer-examples</span>
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<td class="diff-line-num new new_line" data-linenumber="147" 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="LC147" class="line" lang="plaintext">Architecture: all</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">Enhances: sim4db,</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> atac</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">Description: sample data for kmer suite of tools for DNA sequence analysis</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> The kmer package is a suite of tools for DNA sequence analysis.</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> It provides tools for searching (ESTs, mRNAs, sequencing reads);</span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> aligning (ESTs, mRNAs, whole genomes); and a variety of analyses</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> based on kmers.</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> This package contains a test data set as well as sample scripts</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> running some test suite provided by Debian also as autopkgtest.</span></pre>
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<a href="https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d#e8db7227a188eedebdce52697849829e703cb187"><strong>debian/kmer-examples.README.Debian</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">This package provides test data for the kmer components atac and sim4db</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"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">To test atac run:</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"> sh /usr/share/doc/atac/atac-unit-test</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">To test sim4db run:</span>
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9
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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"> sh /usr/share/doc/sim4db/sim4db-unit-test</span></pre>
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<a href="https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d#90b669d683dd3181cfb62aeef460d13896f7ff28"><strong>debian/kmer-examples.docs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/tests/test-data/test_data.tar.gz</span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.sim4db</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">debian/tests/sim4db-unit-test</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">debian/tests/test-data/test_data.tar.gz</span>
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4
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">debian/README.test</span></pre>
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<li id="8bead32e7e58d25ada9d9a6c43de1bfd8d7b4058">
<a href="https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d#8bead32e7e58d25ada9d9a6c43de1bfd8d7b4058"><strong>debian/tests/atac-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">@@ -6,9 +6,19 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then</td>
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6
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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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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;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">ORIGDIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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9
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$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> /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.tar.gz <span class="nb" style="color: #0086b3;">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xzvf</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz<span class="p">;</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-e</span> /usr/share/doc/kmer-examples/test_data.tar.gz <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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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">TARFILE</span><span class="o" style="font-weight: 600;">=</span>/usr/share/doc/kmer-examples/test_data.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-e</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">ORIGDIR</span><span class="k" style="font-weight: 600;">}</span>/debian/tests/test-data/test_data.tar.gz <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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">TARFILE</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">ORIGDIR</span><span class="k" style="font-weight: 600;">}</span>/debian/tests/test-data/test_data.tar.gz</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please install package kmer-examples to run this script"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xaf</span> <span class="nv" style="color: teal;">$TARFILE</span></span>
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12
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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="c" style="color: #998; font-style: italic;"># Run atac:</span></span>
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14
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell">atac <span class="nt" style="color: navy;">-meryldir</span> meryldir <span class="nt" style="color: navy;">-dir</span> results <span class="nt" style="color: navy;">-id1</span> Lepr <span class="nt" style="color: navy;">-seq1</span> GCF_000195855.1_ASM19585v1_genomic.fna <span class="se" style="color: #d14;">\</span></span>
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<li id="250298e80304390409b063185886417f177a00db">
<a href="https://salsa.debian.org/med-team/kmer/compare/2467bacf66b1017368550f041b8b0f638164e256...1dc82e0f62c19816f72ab2e3f62d4efd160f756d#250298e80304390409b063185886417f177a00db"><strong>debian/tests/sim4db-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">@@ -6,9 +6,19 @@ if [ "$AUTOPKGTEST_TMP" = "" ]; then</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">$(</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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: teal;">ORIGDIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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9
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test_data.tar.gz <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;">tar</span> <span class="nt" style="color: navy;">-xzvf</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz<span class="p">;</span> <span class="nb" style="color: #0086b3;">rm</span> <span class="k" style="font-weight: 600;">*</span>.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-e</span> /usr/share/doc/kmer-examples/test_data.tar.gz <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="LC12" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">TARFILE</span><span class="o" style="font-weight: 600;">=</span>/usr/share/doc/kmer-examples/test_data.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="k" style="font-weight: 600;"> if</span> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-e</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">ORIGDIR</span><span class="k" style="font-weight: 600;">}</span>/debian/tests/test-data/test_data.tar.gz <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: teal;">TARFILE</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">ORIGDIR</span><span class="k" style="font-weight: 600;">}</span>/debian/tests/test-data/test_data.tar.gz</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"> <span class="k" style="font-weight: 600;">else</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Please install package kmer-examples to run this script"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="k" style="font-weight: 600;">fi</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">tar</span> <span class="nt" style="color: navy;">-xaf</span> <span class="nv" style="color: teal;">$TARFILE</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></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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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Run sim4db</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Testing sim4 for intra-species alignment...</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;">"</span></span>
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