generated docs update for recent changes

ICGC-TCGA-PanCancer · Mar 5, 2014 · 19078dc · 19078dc
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diff --git a/docs/pod_html/PCAP.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/PCAP/Bam.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/PCAP/Bwa.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/PCAP/Bwa/Meta.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/PCAP/Cli.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/PCAP/SRA.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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
@@ -165,6 +165,14 @@ <h2><a class='u' href='#___top' title='click to go to top of document'
 <pre>  bam object (with info prepopulated)
   study_name
   aliquot_id from BAM RG header SM tag</pre>
+
+<dt><a name="bash_script"
+>bash_script</a></dt>
+
+<dd>
+<p>Takes output path and list of submission UUIDs.</p>
+
+<p>Generates a bash script that can be run to complete GNOS upload with resume capabilities.</p>
 </dd>
 </dl>
 <p class="backlinkbottom"><b><a name="___bottom" href="../index.html" title="All Documents">&lt;&lt;</a></b></p>

diff --git a/docs/pod_html/PCAP/Threaded.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/bam_to_sra_sub.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/bwa_aln.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/bwa_mem.html b/docs/pod_html/bwa_mem.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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/diff_bams.html b/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  3 23:33:40 2014 GMT.
+  under Perl v5.016003 at Wed Mar  5 22:50:11 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

diff --git a/docs/pod_html/index.html b/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  3 23:33:40 2014 GMT, which is Mon Mar  3 23:33:40 2014 local time.</p>
+<br >At Wed Mar  5 22:50:11 2014 GMT, which is Wed Mar  5 22:50:11 2014 local time.</p>
 
 </body></html>
diff --git a/docs/reports_html/coverage.html b/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">2014-03-03 23:33:37</td>
+<td class="sv" align="left" colspan="4">2014-03-05 22:50:07</td>
 </tr>
 <tr>
 <td class="sh" align="right">Perl version:</td>
@@ -106,25 +106,25 @@ <h1> Coverage Summary </h1>
 
 
 
-<td class="c1" title="114 / 143">
+<td class="c1" title="115 / 145">
 
 
-83.2
+82.8
 
 </td>
 
 
 
-<td class="c3" title="58 / 58">
+<td class="c3" title="59 / 59">
 
 
 100.0
 
 </td>
 
 
-<td class="c1" title="346 / 467">
-82.4
+<td class="c1" title="348 / 470">
+82.3
 </td>
 </tr>
 
@@ -355,25 +355,25 @@ <h1> Coverage Summary </h1>
 
 
 
-<td class="c0" title="20 / 39">
+<td class="c0" title="21 / 41">
 
 
-<a href="lib-PCAP-SRA-pm--subroutine.html"> 51.3 </a>
+<a href="lib-PCAP-SRA-pm--subroutine.html"> 51.2 </a>
 
 </td>
 
 
 
-<td class="c3" title="18 / 18">
+<td class="c3" title="19 / 19">
 
 
 <a href="lib-PCAP-SRA-pm--subroutine.html"> 100.0 </a>
 
 </td>
 
 
-<td class="c0" title="47 / 101">
-46.5
+<td class="c0" title="49 / 104">
+47.1
 </td>
 </tr>
 

diff --git a/docs/reports_html/index.html b/docs/reports_html/index.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">2014-03-03 23:33:37</td>
+<td class="sv" align="left" colspan="4">2014-03-05 22:50:07</td>
 </tr>
 <tr>
 <td class="sh" align="right">Perl version:</td>
@@ -106,25 +106,25 @@ <h1> Coverage Summary </h1>
 
 
 
-<td class="c1" title="114 / 143">
+<td class="c1" title="115 / 145">
 
 
-83.2
+82.8
 
 </td>
 
 
 
-<td class="c3" title="58 / 58">
+<td class="c3" title="59 / 59">
 
 
 100.0
 
 </td>
 
 
-<td class="c1" title="346 / 467">
-82.4
+<td class="c1" title="348 / 470">
+82.3
 </td>
 </tr>
 
@@ -355,25 +355,25 @@ <h1> Coverage Summary </h1>
 
 
 
-<td class="c0" title="20 / 39">
+<td class="c0" title="21 / 41">
 
 
-<a href="lib-PCAP-SRA-pm--subroutine.html"> 51.3 </a>
+<a href="lib-PCAP-SRA-pm--subroutine.html"> 51.2 </a>
 
 </td>
 
 
 
-<td class="c3" title="18 / 18">
+<td class="c3" title="19 / 19">
 
 
 <a href="lib-PCAP-SRA-pm--subroutine.html"> 100.0 </a>
 
 </td>
 
 
-<td class="c0" title="47 / 101">
-46.5
+<td class="c0" title="49 / 104">
+47.1
 </td>
 </tr>
 

diff --git a/docs/reports_html/lib-PCAP-Bwa-pm.html b/docs/reports_html/lib-PCAP-Bwa-pm.html
@@ -1160,7 +1160,7 @@ <h1> File Coverage </h1>
 
 </td>
 
-<td class="s"> <span class="word">const</span>&nbsp;<span class="word">my</span> <span class="symbol">$BAMSORT</span> <span class="operator">=&gt;</span> <span class="literal">q{ fixmate=1 inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam inputthreads=%s outputthreads=%s}</span><span class="structure">;</span> </td>
+<td class="s"> <span class="word">const</span>&nbsp;<span class="word">my</span> <span class="symbol">$BAMSORT</span> <span class="operator">=&gt;</span> <span class="literal">q{ inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam inputthreads=%s outputthreads=%s}</span><span class="structure">;</span> </td>
 </tr>
 
 <tr>
-Original file line number
+Diff line change
@@ Expand Up / @@ -1160,7 +1160,7 @@ <h1> File Coverage </h1> @@
     </td>
-    <td class="s"> <span class="word">const</span>&nbsp;<span class="word">my</span> <span class="symbol">$BAMSORT</span> <span class="operator">=&gt;</span> <span class="literal">q{ fixmate=1 inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam inputthreads=%s outputthreads=%s}</span><span class="structure">;</span> </td>
+    <td class="s"> <span class="word">const</span>&nbsp;<span class="word">my</span> <span class="symbol">$BAMSORT</span> <span class="operator">=&gt;</span> <span class="literal">q{ inputformat=sam level=1 tmpfile=%s_tmp O=%s_sorted.bam inputthreads=%s outputthreads=%s}</span><span class="structure">;</span> </td>
     </tr>
     <tr>
@@ Expand Down @@