Merge pull request #25 from cancerit/dev

Revises gender determination to be based on normal sample only.

perl/MANIFEST

@@ -20,14 +20,15 @@ docs/pod_html/CN_to_VCF.html
 docs/pod_html/failed_cn_csv.html
 docs/pod_html/index.html
 docs/pod_html/Sanger/CGP/Ascat.html
+docs/reports_html/blib-lib-Sanger-CGP-Ascat-pm--subroutine.html
+docs/reports_html/blib-lib-Sanger-CGP-Ascat-pm.html
 docs/reports_html/common.js
+docs/reports_html/cover.14
 docs/reports_html/cover.css
 docs/reports_html/coverage.html
 docs/reports_html/css.js
 docs/reports_html/digests
 docs/reports_html/index.html
-docs/reports_html/lib-Sanger-CGP-Ascat-pm--subroutine.html
-docs/reports_html/lib-Sanger-CGP-Ascat-pm.html
 docs/reports_html/standardista-table-sorting.js
 docs/reports_text/coverage.txt
 lib/Sanger/CGP/Ascat.pm

perl/MYMETA.json

@@ -37,5 +37,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v1.5.0"
+   "version" : "v1.5.1"
 }

perl/MYMETA.yml

@@ -19,4 +19,4 @@ no_index:
     - inc
 requires:
   Const::Fast: '0.014'
-version: v1.5.0
+version: v1.5.1

perl/lib/Sanger/CGP/Ascat.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '1.5.0';
+our $VERSION = '1.5.1';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>

perl/lib/Sanger/CGP/Ascat/Implement.pm

@@ -284,40 +284,29 @@ sub determine_gender {
   }
 
   my $command = _which('alleleCounter');
-  $command .= sprintf $ALLELE_COUNT_PARA, $options->{'tumour'}, File::Spec->catfile($options->{'tmp'}, 'tumour_gender.tsv'), $gender_loci;
-  $command .= '-m '.$options->{'minbasequal'} if exists $options->{'minbasequal'};
-  system($command);
-  my $tum_gender = _parse_gender_results(File::Spec->catfile($options->{'tmp'}, 'tumour_gender.tsv'));
-  $command = _which('alleleCounter');
   $command .= sprintf $ALLELE_COUNT_PARA, $options->{'normal'}, File::Spec->catfile($options->{'tmp'}, 'normal_gender.tsv'), $gender_loci;
   $command .= '-m '.$options->{'minbasequal'} if exists $options->{'minbasequal'};
   system($command);
   my $norm_gender = _parse_gender_results(File::Spec->catfile($options->{'tmp'}, 'normal_gender.tsv'));
-  if($tum_gender ne $norm_gender) {
-    die "Gender loci gacve incolclusive results see $options->{tmp}/*_gender.tsv";
-  }
-  return $tum_gender;
+  return $norm_gender;
 }
 
 sub _parse_gender_results {
   my $file = shift @_;
-  my $male_loci = 0;
-  my $total_loci = 0;
+  my $gender = 'XX';
   open my $fh, '<', $file;
   while(my $line = <$fh>) {
     next if($line =~ m/^#/);
     chomp $line;
     #CHR	POS	Count_A	Count_C	Count_G	Count_T	Good_depth
     my ($chr, $pos, $a, $c, $g, $t, $depth) = split /\t/, $line;
     # all we really care about is the depth
-    $male_loci++ if($depth > 5);
-    $total_loci++;
+    if($depth > 5) {
+      $gender = 'XY';
+      last; # presence of ANY male loci in normal is sufficient, we shouldn't be using this to check for 'matchedness'
+    }
   }
   close $fh;
-  my $gender = 'XX';
-  if($male_loci/$total_loci >= 0.5) {
-    $gender = 'XY';
-  }
   return $gender;
 }