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Fixed #14 as built successfully from scratch on vanilla Ubuntu 12.04 VM new release 0.2 for tagging.
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‎MANIFEST

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@@ -45,6 +45,7 @@ docs/reports_html/lib-PCAP-Bwa-pm.html
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docs/reports_html/lib-PCAP-Cli-pm--branch.html
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docs/reports_html/lib-PCAP-Cli-pm--subroutine.html
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docs/reports_html/lib-PCAP-Cli-pm.html
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docs/reports_html/lib-PCAP-pm--branch.html
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docs/reports_html/lib-PCAP-pm--subroutine.html
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docs/reports_html/lib-PCAP-pm.html
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docs/reports_html/lib-PCAP-SRA-pm--branch.html

‎docs/pod_html/PCAP.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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using Pod::Simple::PullParser v3.28,
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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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If you want to change this HTML document, you probably shouldn't do that
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by changing it directly. Instead, see about changing the calling options

‎docs/pod_html/PCAP/Bam.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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by changing it directly. Instead, see about changing the calling options

‎docs/pod_html/PCAP/Bwa.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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by changing it directly. Instead, see about changing the calling options

‎docs/pod_html/PCAP/Bwa/Meta.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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using Pod::Simple::PullParser v3.28,
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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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by changing it directly. Instead, see about changing the calling options

‎docs/pod_html/PCAP/Cli.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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by changing it directly. Instead, see about changing the calling options

‎docs/pod_html/PCAP/SRA.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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‎docs/pod_html/PCAP/Threaded.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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‎docs/pod_html/bam_to_sra_sub.html

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<!--
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generated by Pod::Simple::HTML v3.28,
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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<pre> Required parameters:
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-outdir -o Folder to output result to.
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-study -s Study reference in repository
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-gnos -g GNOS upload server, e.g.
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https://gtrepo-ebi.annailabs.com
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Optional:
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-type -t Only required if not encoded in readgroup LB tag.

‎docs/pod_html/bwa_aln.html

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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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by changing it directly. Instead, see about changing the calling options

‎docs/pod_html/bwa_mem.html

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<html><head><title>bwa_aln.pl</title>
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<html><head><title>bwa_mem.pl</title>
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<meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" >
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<link rel="stylesheet" title="blkbluw" type="text/css" href="_blkbluw.css" media="all" >
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<link rel="alternate stylesheet" title="blkmagw" type="text/css" href="_blkmagw.css" media="all" >
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<!--
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generated by Pod::Simple::HTML v3.28,
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using Pod::Simple::PullParser v3.28,
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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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name="NAME"
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>NAME</a></h1>
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<p>bwa_aln.pl - Align a set of lanes to specified reference with single command.</p>
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<p>bwa_mem.pl - Align a set of lanes to specified reference with single command.</p>
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<h1><a class='u' href='#___top' title='click to go to top of document'
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name="SYNOPSIS"
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-man -m Full documentation.
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File list can be full file names or wildcard, e.g.
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bwa_aln.pl -t 16 -r some/genome.fa.gz -o myout -s sample input/*.fq.gz
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bwa_mem.pl -t 16 -r some/genome.fa.gz -o myout -s sample input/*.bam
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Run with &#39;-m&#39; for possible input file types.</pre>
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>f[ast]q</a></dt>
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<dd>
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<p>A standard uncompressed fastq file. Requires a pair of inputs with standard suffix of &#39;_1&#39; and &#39;_2&#39; immediately prior to &#39;.f[ast]q&#39;.</p>
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<p>A standard uncompressed fastq file. Requires a pair of inputs with standard suffix of &#39;_1&#39; and &#39;_2&#39; immediately prior to &#39;.f[ast]q&#39; or an interleaved f[ast]q file where read 1 and 2 are adjacent in the file.</p>
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>bam</a></dt>
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<p>A list of single lane BAM files, no information is taken from the headers.</p>
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<p><b>This method has additional processing converted to *.fq.gz to give common start point.</b></p>
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<p>A list of single lane BAM files, RG line is transfered to aligned files.</p>
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</dd>
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</dl>
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<h1><a class='u' href='#___top' title='click to go to top of document'
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name="DESCRIPTION"
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>DESCRIPTION</a></h1>
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<p><b>bwa_aln.pl</b> will attempt to run all mapping steps for BWA ALN and subsequent duplicate marking automatically.</p>
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<p><b>bwa_mem.pl</b> will attempt to run all mapping steps for BWA-mem, as well as subsequent merging and duplicate marking automatically.</p>
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<p class="backlinkbottom"><b><a name="___bottom" href="index.html" title="All Documents">&lt;&lt;</a></b></p>
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<!-- end doc -->

‎docs/pod_html/diff_bams.html

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under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
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under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
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‎docs/pod_html/index.html

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<p class='contentsfooty'>Generated by Pod::Simple::HTMLBatch v3.28 under Perl v5.016003
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<br >At Mon Mar 10 09:38:35 2014 GMT, which is Mon Mar 10 09:38:35 2014 local time.</p>
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<br >At Fri Mar 14 16:34:22 2014 GMT, which is Fri Mar 14 16:34:22 2014 local time.</p>
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</body></html>

‎docs/reports_html/coverage.html

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</tr>
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<tr>
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<td class="sh" align="right">Report date:</td>
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<td class="sv" align="left" colspan="4">2014-03-10 09:38:33</td>
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<td class="sv" align="left" colspan="4">2014-03-14 16:34:19</td>
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<td class="c1" title="174 / 274">
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<td class="c1" title="115 / 146">
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n/a
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<a href="lib-PCAP-pm--branch.html"> 0.0 </a>
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<a href="lib-PCAP-pm--subroutine.html"> 100.0 </a>
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<a href="lib-PCAP-pm--subroutine.html"> 75.0 </a>
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<a href="lib-PCAP-pm--subroutine.html"> 50.0 </a>
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<a href="lib-PCAP-Bwa-pm--branch.html"> 100.0 </a>
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<a href="lib-PCAP-Bwa-pm--branch.html"> 92.3 </a>
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<a href="lib-PCAP-SRA-pm--branch.html"> 20.5 </a>
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<a href="lib-PCAP-SRA-pm--branch.html"> 19.6 </a>
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46.2
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