Fixed #14 as built successfully from scratch on vanilla Ubuntu 12.04 …

…VM new release 0.2 for tagging.

MANIFEST

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

docs/pod_html/PCAP.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/PCAP/Bam.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/PCAP/Bwa.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/PCAP/Bwa/Meta.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/PCAP/Cli.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/PCAP/SRA.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/PCAP/Threaded.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/bam_to_sra_sub.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options
@@ -58,6 +58,8 @@ <h1><a class='u' href='#___top' title='click to go to top of document'
 <pre>  Required parameters:
     -outdir    -o   Folder to output result to.
     -study     -s   Study reference in repository
+    -gnos      -g   GNOS upload server, e.g.
+                      https://gtrepo-ebi.annailabs.com
 
   Optional:
     -type      -t   Only required if not encoded in readgroup LB tag.

docs/pod_html/bwa_aln.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/bwa_mem.html

@@ -1,4 +1,4 @@
-<html><head><title>bwa_aln.pl</title>
+<html><head><title>bwa_mem.pl</title>
 <meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1" >
 <link rel="stylesheet" title="blkbluw" type="text/css" href="_blkbluw.css" media="all" >
 <link rel="alternate stylesheet" title="blkmagw" type="text/css" href="_blkmagw.css" media="all" >
@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options
@@ -52,7 +52,7 @@ <h1><a class='u' href='#___top' title='click to go to top of document'
 name="NAME"
 >NAME</a></h1>
 
-<p>bwa_aln.pl - Align a set of lanes to specified reference with single command.</p>
+<p>bwa_mem.pl - Align a set of lanes to specified reference with single command.</p>
 
 <h1><a class='u' href='#___top' title='click to go to top of document'
 name="SYNOPSIS"
@@ -79,7 +79,7 @@ <h1><a class='u' href='#___top' title='click to go to top of document'
     -man       -m   Full documentation.
 
   File list can be full file names or wildcard, e.g.
-    bwa_aln.pl -t 16 -r some/genome.fa.gz -o myout -s sample input/*.fq.gz
+    bwa_mem.pl -t 16 -r some/genome.fa.gz -o myout -s sample input/*.bam
 
   Run with &#39;-m&#39; for possible input file types.</pre>
 
@@ -154,7 +154,7 @@ <h2><a class='u' href='#___top' title='click to go to top of document'
 >f[ast]q</a></dt>
 
 <dd>
-<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>
+<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>
 
 <dt><a name="f[ast]q.gz"
 >f[ast]q.gz</a></dt>
@@ -166,17 +166,15 @@ <h2><a class='u' href='#___top' title='click to go to top of document'
 >bam</a></dt>
 
 <dd>
-<p>A list of single lane BAM files, no information is taken from the headers.</p>
-
-<p><b>This method has additional processing converted to *.fq.gz to give common start point.</b></p>
+<p>A list of single lane BAM files, RG line is transfered to aligned files.</p>
 </dd>
 </dl>
 
 <h1><a class='u' href='#___top' title='click to go to top of document'
 name="DESCRIPTION"
 >DESCRIPTION</a></h1>
 
-<p><b>bwa_aln.pl</b> will attempt to run all mapping steps for BWA ALN and subsequent duplicate marking automatically.</p>
+<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>
 <p class="backlinkbottom"><b><a name="___bottom" href="index.html" title="All Documents">&lt;&lt;</a></b></p>
 
 <!-- end doc -->

docs/pod_html/diff_bams.html

@@ -21,7 +21,7 @@
 <!--
   generated by Pod::Simple::HTML v3.28,
   using Pod::Simple::PullParser v3.28,
-  under Perl v5.016003 at Mon Mar 10 09:38:35 2014 GMT.
+  under Perl v5.016003 at Fri Mar 14 16:34:22 2014 GMT.
 
  If you want to change this HTML document, you probably shouldn't do that
    by changing it directly.  Instead, see about changing the calling options

docs/pod_html/index.html

@@ -59,6 +59,6 @@ <h1>Perl Documentation</h1>
 
 
 <p class='contentsfooty'>Generated by Pod::Simple::HTMLBatch v3.28 under Perl v5.016003
-<br >At Mon Mar 10 09:38:35 2014 GMT, which is Mon Mar 10 09:38:35 2014 local time.</p>
+<br >At Fri Mar 14 16:34:22 2014 GMT, which is Fri Mar 14 16:34:22 2014 local time.</p>
 
 </body></html>

docs/reports_html/coverage.html

@@ -28,7 +28,7 @@ <h1> Coverage Summary </h1>
 </tr>
 <tr>
 <td class="sh" align="right">Report date:</td>
-<td class="sv" align="left" colspan="4">2014-03-10 09:38:33</td>
+<td class="sv" align="left" colspan="4">2014-03-14 16:34:19</td>
 </tr>
 <tr>
 <td class="sh" align="right">Perl version:</td>
@@ -97,34 +97,34 @@ <h1> Coverage Summary </h1>
 
 
 
-<td class="c1" title="174 / 266">
+<td class="c1" title="174 / 274">
 
 
-78.2
+75.9
 
 </td>
 
 
 
-<td class="c1" title="115 / 145">
+<td class="c1" title="115 / 146">
 
 
-82.8
+82.2
 
 </td>
 
 
 
-<td class="c3" title="59 / 59">
+<td class="c2" title="59 / 60">
 
 
-100.0
+98.3
 
 </td>
 
 
-<td class="c1" title="348 / 470">
-82.3
+<td class="c1" title="348 / 480">
+80.6
 </td>
 </tr>
 
@@ -141,34 +141,34 @@ <h1> Coverage Summary </h1>
 
 
 
-<td>
+<td class="c0" title="0 / 4">
 
 
-n/a
+<a href="lib-PCAP-pm--branch.html">  0.0 </a>
 
 </td>
 
 
 
-<td class="c3" title="3 / 3">
+<td class="c1" title="3 / 4">
 
 
-<a href="lib-PCAP-pm--subroutine.html"> 100.0 </a>
+<a href="lib-PCAP-pm--subroutine.html"> 75.0 </a>
 
 </td>
 
 
 
-<td class="c3" title="1 / 1">
+<td class="c0" title="1 / 2">
 
 
-<a href="lib-PCAP-pm--subroutine.html"> 100.0 </a>
+<a href="lib-PCAP-pm--subroutine.html"> 50.0 </a>
 
 </td>
 
 
-<td class="c3" title="4 / 4">
-100.0
+<td class="c0" title="4 / 10">
+40.0
 </td>
 </tr>
 
@@ -223,10 +223,10 @@ <h1> Coverage Summary </h1>
 
 
 
-<td class="c3" title="0 / 24">
+<td class="c2" title="0 / 26">
 
 
-<a href="lib-PCAP-Bwa-pm--branch.html"> 100.0 </a>
+<a href="lib-PCAP-Bwa-pm--branch.html"> 92.3 </a>
 
 </td>
 
@@ -249,8 +249,8 @@ <h1> Coverage Summary </h1>
 </td>
 
 
-<td class="c3" title="17 / 44">
-100.0
+<td class="c2" title="17 / 46">
+95.7
 </td>
 </tr>
 
@@ -346,10 +346,10 @@ <h1> Coverage Summary </h1>
 
 
 
-<td class="c0" title="9 / 44">
+<td class="c0" title="9 / 46">
 
 
-<a href="lib-PCAP-SRA-pm--branch.html"> 20.5 </a>
+<a href="lib-PCAP-SRA-pm--branch.html"> 19.6 </a>
 
 </td>
 
@@ -372,8 +372,8 @@ <h1> Coverage Summary </h1>
 </td>
 
 
-<td class="c0" title="49 / 104">
-47.1
+<td class="c0" title="49 / 106">
+46.2
 </td>
 </tr>