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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/bioperl-run">Debian Med / bioperl-run</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/1d0816c1e6114efaa1af54d1f79568a410ad9a8a">1d0816c1</a></strong>
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<span>by Pranav Ballaney</span>
<i>at 2020-03-30T16:38:24+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change kalign command string to input via stdin
It fails to take input via the -in flag during testing
</pre>
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<h4>1 changed file:</h4>
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<a href="#addaa1c3a87398a6ba36723589208ded2b878da8">
lib/Bio/Tools/Run/Alignment/Kalign.pm
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<h4>Changes:</h4>
<li id="addaa1c3a87398a6ba36723589208ded2b878da8">
<a href="https://salsa.debian.org/med-team/bioperl-run/-/commit/1d0816c1e6114efaa1af54d1f79568a410ad9a8a#addaa1c3a87398a6ba36723589208ded2b878da8"><strong>lib/Bio/Tools/Run/Alignment/Kalign.pm</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">@@ -339,7 +339,7 @@ sub align {</td>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="perl"><span class="k" style="font-weight: 600;">sub </span><span class="nf" style="color: #900; font-weight: 600;">_run</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="p">(</span><span class="nv" style="color: #008080;">$self</span><span class="p">,</span><span class="nv" style="color: #008080;">$infilename</span><span class="p">,</span><span class="nv" style="color: #008080;">$params</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">@_</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$commandstring</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;"><span class="idiff left">$self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">executable</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff">"</span></span><span class="s2" style="color: #d14;"><span class="idiff"> -in </span></span><span class="si" style="color: #d14;"><span class="idiff right">$infilename</span></span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$params</span><span class="p">";</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$commandstring</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">"</span></span><span class="s2" style="color: #d14;"><span class="idiff">cat </span></span><span class="si" style="color: #d14;"><span class="idiff">$infilename</span></span><span class="s2" style="color: #d14;"><span class="idiff"> | </span></span><span class="p"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nv" style="color: #008080;"><span class="idiff">$self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="nv" style="color: #008080;"><span class="idiff">executable</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="p"><span class="idiff right">"</span></span><span class="s2" style="color: #d14;"> </span><span class="si" style="color: #d14;">$params</span><span class="p">";</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="perl"> </span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="perl"> <span class="nv" style="color: #008080;">$self</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">debug</span><span class="p">(</span> <span class="p">"</span><span class="s2" style="color: #d14;">kalign command = </span><span class="si" style="color: #d14;">$commandstring</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\n</span><span class="p">");</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="perl"></span>
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