Merge pull request #510 from wtsi-npg/devel

merge devel to master for release 64.6.2

Changes

@@ -1,5 +1,7 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - QC viewer changes for genotype call
+
 release 64.6.1
  - tweak to GbS library type check in genotype call as arrived as GBS (now case-insensitive).
  - Exit rna seqc gracefully if bam has no reads

npg_qc_viewer/MANIFEST

@@ -48,6 +48,7 @@ root/src/ui_checks/contamination.tt2
 root/src/ui_checks/fastqcheck_visuals.tt2
 root/src/ui_checks/gc_bias.tt2
 root/src/ui_checks/gc_fraction.tt2
+root/src/ui_checks/genotype_call.tt2
 root/src/ui_checks/genotype.tt2
 root/src/ui_checks/insert_size.tt2
 root/src/ui_checks/pulldown_metrics.tt2

npg_qc_viewer/root/src/about.tt2

@@ -18,6 +18,7 @@
   <li>fastqcheck files rendering as heatmaps</li>
   <li>gc fraction</li>
   <li>genotype - sample ID check (Sequenom genotypes)</li>
+  <li>genotype call (subset)</li>
   <li>insert size</li>
   <li>qc bias</li>
   <li>qX yield (threshold quality 20)</li>

npg_qc_viewer/root/src/about_qc_checks.tt2

@@ -118,6 +118,42 @@ Any close genotype matches found under a different sample name, allowing homozyg
 <br/><br/>
 
 <br/>
+<a name="genotype call_check"></a>
+ <h3>Genotype call metrics</h3>
+
+<br/>
+<h4>Description</h4>
+Metrics generated as part of calling genotypes at a set of sites specified by the genotype plex name.
+<br/>
+<br/>
+
+<h4>Output Fields</h4>
+<br/>
+<table style="margin-left: 5%; margin-right: 20%;">
+<tr><th>Field</th><th>Description</th></tr>
+<tr>
+  <td>Genotypes attempted</td>
+  <td style="padding: 0 0 5px 10px;">The number genotype sites where a call is attempted.</td>
+</tr>
+<tr>
+  <td>Genotype call rate</td>
+  <td style="padding: 0 0 5px 10px;">The sites called divided by the number genotype sites attempted.</td>
+</tr>
+<tr>
+  <td>Genotype pass rate</td>
+  <td style="padding: 0 0 5px 10px;">The sites called and passing plex specific filters divided by the number genotype sites attempted.</td>
+</tr>
+<tr>
+  <td>Sex markers attempted</td>
+  <td style="padding: 0 0 5px 10px;">Number of sex markers (if present).</td>
+</tr>
+<tr>
+  <td>Sex</td>
+  <td style="padding: 0 0 5px 10px;">M or F for each male or female call (if sex markers present).</td>
+</tr>
+</table>
+
+<br/><br/>
 
 <a name="rna seqc_check"></a>
  <h3>RNA-SeQC metrics</h3>

npg_qc_viewer/root/src/ui_checks/genotype_call.tt2

@@ -0,0 +1,31 @@
+[% USE Number.Format(THOUSANDS_SEP=',') %]
+
+<div class="data_table">
+<table title="genotype call">
+<tr>
+  <th class="laligned">Genotype plex name</th> <td>[% check.gbs_plex_name %]</td>
+</tr>
+[%- IF check.criterion.defined -%]
+<tr><th class="laligned">Pass criterion</th> <td>[% check.criterion FILTER html %]</td></tr>
+[%- END -%]
+[%- IF check.gbs_plex_path.defined -%]
+<tr><th class="laligned">Genotype plex path</th> <td>[% check.gbs_plex_path %]</td></tr>
+[%- END -%]
+[%- IF check.comments.defined -%]
+<tr><th class="laligned">comments</th><td>[% check.comments %]</td></tr>
+[%- END -%]
+</table>
+</div>
+
+<div class="data_table">
+<table title="genotype call section two">
+<caption>Genotype results</caption>
+<tr>
+  <th class="laligned">Genotypes attempted</th><td>[% check.genotypes_attempted %]</td>
+  <th class="laligned">Genotype call rate</th><td>[% check.genotype_call_rate %]</td>
+  <th class="laligned">Genotype pass rate</th><td>[% check.genotype_passed_rate %]</td>
+  <th class="laligned">Sex markers attempted</th><td>[% check.sex_markers_attempted %]</td>
+  <th class="laligned">Sex</th><td>[% check.sex %]</td>
+</tr>
+</table>
+</div>

npg_qc_viewer/root/src/ui_lanes/checks_header.tt2

@@ -6,6 +6,7 @@
       contamination    = 'top two'
       gc_bias          = '<span class="nbsp">plot created</span><br />'
       gc_fraction      = 'fraction,<br />%'
+      genotype_call    = 'call rate<br />pass rate<br />'
       genotype         = 'match<br/><span class="dark_blue nbsp">mean cvg.<br/>depth<br/></span>'
       insert_size      = 'quartiles,<br />bases'
       pulldown_metrics = '<span class="nbsp">coverage at 20X, %</span><br /><span class="nbsp">mean depth per Gb</span><br /><span class="dark_blue nbsp">on bait bases, %</span><br /><span class="dark_blue nbsp">on target bases, %</span>'
@@ -25,7 +26,7 @@
 <th[% row_span_string %]>Lane<br />No</th>
 [% IF has_plexes %]<th[% row_span_string %]>Tag</th>[% END %]
 [%- FOREACH check_name IN checks_list -%]
-  [% IF check_name.match('genotype') && !check_name.match('W30467') %]
+  [% IF (check_name.match('genotype') && !check_name.match('call')) && !check_name.match('W30467') %]
     [% NEXT %]
   [% END %]
   [% IF check_name.match('genotype') || check_name == "rna seqc" || check_name == "upstream tags" || check_name == "verify bam id" || check_name.match('tag metrics') %]
@@ -40,7 +41,7 @@
 </tr>
 <tr>
   [%- FOREACH check_name IN checks_list; class_name = map.$check_name %]
-  [% IF check_name.match('genotype') && !check_name.match('W30467') %]
+  [% IF (check_name.match('genotype') && !check_name.match('call')) && !check_name.match('W30467') %]
     [% NEXT %]
   [% END %]
 <th class="check_labels">[% labels.$class_name %]</th>

npg_qc_viewer/root/src/ui_lanes/lane.tt2

@@ -31,7 +31,7 @@
 [%- END -%]
 
 [%- FOREACH check_name IN checks_list;
-      IF check_name.match('genotype') && !check_name.match('W30467');
+      IF (check_name.match('genotype') && !check_name.match('call')) && !check_name.match('W30467');
         NEXT;
       END;
 
@@ -449,3 +449,15 @@ END
 [%  END %]
 [% END %]
 
+[% BLOCK genotype_call %]
+[%  IF result.genotype_call_rate.defined %]
+      <span>[% result.genotype_call_rate %]<br/></span>
+[%  ELSE %]
+      <span>na</span>
+[%  END %]
+[%  IF result.genotype_passed_rate.defined %]
+      <span>[% result.genotype_passed_rate %]<br/></span>
+[%  ELSE %]
+      <span>na</span>
+[%  END %]
+[%-   END -%]