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<h3>
Étienne Mollier pushed to branch master
at <a href="https://salsa.debian.org/med-team/bioperl-run">Debian Med / bioperl-run</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4">86ba0c47</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2020-12-04T23:57:46+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">flag tests needing adaptations
These adaptations are due to the use of a dataset different from
the reference data in use by bioperl-run upstream.
</pre>
</li>
</ul>
<h4>1 changed file:</h4>
<ul>
<li class="file-stats">
<a href="#b472300eb19c309e0f4225559c8920ccf1f28829">
debian/patches/alternate-data.patch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="b472300eb19c309e0f4225559c8920ccf1f28829">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/86ba0c476be5118a5cec3cc3e1c2bb62c6f93ff4#b472300eb19c309e0f4225559c8920ccf1f28829"><strong>debian/patches/alternate-data.patch</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">@@ -30,3 +30,26 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> ($gene_bed) = `find /usr -name 'knownGene.hg18.chr21.bed' 2>/dev/null`;</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> ($mm8_genome) = `find /usr -name 'mouse.mm8.genome' 2>/dev/null`;</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> ($mm9_genome) = `find /usr -name 'mouse.mm9.genome' 2>/dev/null`;</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">@@ -326,7 +326,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> open (FILE, $file);</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> my $lines =()= <FILE>;</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> close FILE;</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ TODO: {</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ local $TODO = "maybe adapt reference results to Debian specific dataset";</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> is( $lines, $result_lookup{$command}, " - number of lines");</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> } else {</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> $v && diag(" check can get internal result format matches result file");</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> my $guesser = Bio::Tools::GuessSeqFormat->new( -file => $file );</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="p">@@ -356,8 +359,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> isa_ok( $objres, 'Bio::SeqFeature::Collection',</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> "returned object is correct for command '$command'" );</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> $v && diag(" - correct number of features");</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ TODO: {</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ local $TODO = "maybe adapt reference results to Debian specific dataset";</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> is( scalar $objres->get_all_features, $result_lookup{$command},</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> "correct number of features for command '$command'" );</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> last;</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> m/^fasta$/ && do {</span></pre>
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