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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/npinv">Debian Med / npinv</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1">1b38eb4a</a></strong>
<div>
<span>by Steffen</span>
<i>at 2021-07-11T21:30:38+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Towards lintian-cleanliness.
</pre>
</li>
</ul>
<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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</a>
</li>
<li class="file-stats">
<a href="#35518f41913f4f498424284865f06fc595cd6815">
<span class="new-file">
+
debian/npInv
</span>
</a>
</li>
<li class="file-stats">
<a href="#b6a01dbe7159aae3e783dfff6b72324c268462f1">
<span class="new-file">
+
debian/npInv.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#d7c2e54b8351f2f520394bc596d1a309d226c90b">
<span class="new-file">
+
debian/npinv.dirs
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<li class="file-stats">
<a href="#559681709a84c35683a4a1002e624fca74b4fae9">
<span class="new-file">
+
debian/npinv.install
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</a>
</li>
<li class="file-stats">
<a href="#0dd2faa60bbdc975dbf03df3826162056881ce80">
<span class="new-file">
+
debian/npinv.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="16" 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">@@ -16,7 +16,11 @@ Rules-Requires-Root: no</td>
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<td class="new_line diff-line-num" data-linenumber="16" 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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num" data-linenumber="17" 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="new_line diff-line-num" data-linenumber="17" 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="LC17" class="line" lang="plaintext">Package: npinv</span>
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<td class="old_line diff-line-num" data-linenumber="18" 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="new_line diff-line-num" data-linenumber="18" 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="LC18" class="line" lang="plaintext">Architecture: all</span>
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<td class="new_line diff-line-num old" data-linenumber="19" 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="LC19" class="line" lang="plaintext">Depends: ${misc:Depends}</span>
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<td class="new_line diff-line-num new" data-linenumber="19" 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="LC19" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<td class="new_line diff-line-num new" data-linenumber="20" 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="LC20" class="line" lang="plaintext"> libcommons-math3-java,</span>
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<td class="new_line diff-line-num new" data-linenumber="21" 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="LC21" class="line" lang="plaintext"> libpicard-java,</span>
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<td class="new_line diff-line-num new" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> libhtsjdk-java,</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> jarwrapper</span>
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<td class="new_line diff-line-num" data-linenumber="24" 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="LC24" class="line" lang="plaintext">Description: finds inversions in long DNA segments post alignment</span>
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<td class="new_line diff-line-num" data-linenumber="25" 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="LC25" class="line" lang="plaintext"> npInv accurately detects and genotypes inversions using multiple</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> alignment long reads.</span></pre>
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</li>
<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/npInv.1</span></pre>
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</li>
<li id="35518f41913f4f498424284865f06fc595cd6815">
<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#35518f41913f4f498424284865f06fc595cd6815"><strong>debian/npInv</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</span></span>
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<td class="new_line diff-line-num new" 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="shell">java <span class="nt" style="color: #000080;">-cp</span> /usr/share/java/htsjdk.jar:/usr/share/java/commons-math3.jar:/usr/share/java/picard.jar <span class="nt" style="color: #000080;">-jar</span> /usr/share/java/npInv.jar <span class="nv" style="color: #008080;">$*</span></span></pre>
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<li id="b6a01dbe7159aae3e783dfff6b72324c268462f1">
<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#b6a01dbe7159aae3e783dfff6b72324c268462f1"><strong>debian/npInv.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH NPINV "1" "July 2021" "npInv 1.24" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">npInv \- npInv</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Program function: Read a SE bam file and get the inversion</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Version: 1.24</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fB\-\-output[String]\fR file to write</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">\fB\-\-input[String]\fR file to read</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">optional:</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">\fB\-\-region[String]\fR Specify the region for running.</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Such as chr9:1\-1000 OR chr9 OR all Default[all]</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.PP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-\-minAln[int]\fR minimum size for Alignment & Inv. Default[500]</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-\-IRdatabase[String]\fR An inverted repeat file for the reference in bed format. Default[none]</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-\-min[int]\fR minimum size of an inversion. Default[500]</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-\-max[int]\fR maximum size of an inversion. Default[10000]</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-\-window[int]\fR minimun window size (bp) to merge inversion breakpoints. Default[2000]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">\fB\-\-threshold[int]\fR minimum number of supporting reads for an inversion. Default[3]</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-\-help\fR Show usage</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">For example: java \fB\-jar\fR npInv.jar \fB\-\-input\fR sample.bam \fB\-\-output\fR sample.VCF</span></pre>
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<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#d7c2e54b8351f2f520394bc596d1a309d226c90b"><strong>debian/npinv.dirs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/java</span></pre>
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<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#559681709a84c35683a4a1002e624fca74b4fae9"><strong>debian/npinv.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">npInv</span><span class="o" style="font-weight: 600;">*.</span><span class="n" style="color: #333;">jar</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">java</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">debian</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">npInv</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">bin</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#0dd2faa60bbdc975dbf03df3826162056881ce80"><strong>debian/npinv.links</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/java/npInv-1.24.jar usr/share/java/npInv.jar</span></pre>
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<a href="https://salsa.debian.org/med-team/npinv/-/commit/1b38eb4a4c1fe2724b6346fceb77e0c342debec1#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -4,18 +4,19 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> dh $@</span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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6
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<td class="new_line diff-line-num" 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">CLASSPATH=/usr/share/java/htsjdk.jar:/usr/share/java/picard.jar:/usr/share/java/commons-math3.jar </span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">VERSION=1.24</span>
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7
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<td class="new_line diff-line-num" 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">
8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">override_dh_auto_build:</span>
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8
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<td class="new_line diff-line-num" 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">
9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> ln -s . inversion</span>
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9
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<td class="new_line diff-line-num" 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">
10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> javac -cp $(CLASSPATH) inversion/*.java </span>
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10
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> mkdir -p META-INF</span>
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11
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> cp debian/MANIFEST.MF META-INF</span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> jar cmvf META-INF/MANIFEST.MF npInv.jar inversion/*.class inversion/*.java</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> chmod +x npInv.jar</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> jar cmvf META-INF/MANIFEST.MF npInv<span class="idiff left">-$(VERSION)</span>.jar inversion/*.class <span class="idiff right">#</span>inversion/*.java</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> chmod +x npInv<span class="idiff left right">-$(VERSION)</span>.jar</span>
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14
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> rm -rf META-INF inversion</span>
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15
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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16
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_test:</span>
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17
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> java -cp /usr/share/java/htsjdk.jar:/usr/share/java/commons-math3.jar:/usr/share/java/picard.jar -jar npInv.jar --help</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> java -cp /usr/share/java/htsjdk.jar:/usr/share/java/commons-math3.jar:/usr/share/java/picard.jar -jar npInv<span class="idiff left right">-$(VERSION)</span>.jar --help</span>
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19
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<td class="new_line diff-line-num" data-linenumber="20" 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">
20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">endif</span>
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20
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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21
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_auto_clean:</span>
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