Merge tag 'v5.3.1' into dev

Fix a couple of bugs
cancerit · Mar 1, 2017 · 2e7b74c · 2e7b74c
2 parents eb53a68 + 845e98e
commit 2e7b74c
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Showing 5 changed files with 17 additions and 11 deletions.
diff --git a/perl/bin/brass.pl b/perl/bin/brass.pl
@@ -340,11 +340,12 @@ sub setup {
   }
 
 	if(!defined $opts{'process'} || first { $opts{'process'} eq $_ } (qw(normcn filter grass))) {
-  	Sanger::CGP::Brass::Implement::get_ascat_summary(\%opts);
-  	die "Failed to find 'rho' in $opts{ascat_summary}\n" unless(exists $opts{'Acf'});
-  	die "Failed to find 'Ploidy' in $opts{ascat_summary}\n" unless(exists $opts{'Ploidy'});
-  	die "Failed to find 'GenderChr' in $opts{ascat_summary}\n" unless(exists $opts{'GenderChr'});
-  	die "Failed to find 'GenderChrFound' in $opts{ascat_summary}\n" unless(exists $opts{'GenderChrFound'});
+  	if(Sanger::CGP::Brass::Implement::get_ascat_summary(\%opts)) {
+    	die "Failed to find 'rho' in $opts{ascat_summary}\n" unless(exists $opts{'Acf'});
+    	die "Failed to find 'Ploidy' in $opts{ascat_summary}\n" unless(exists $opts{'Ploidy'});
+    	die "Failed to find 'GenderChr' in $opts{ascat_summary}\n" unless(exists $opts{'GenderChr'});
+    	die "Failed to find 'GenderChrFound' in $opts{ascat_summary}\n" unless(exists $opts{'GenderChrFound'});
+    }
   }
 
 
@@ -383,10 +384,10 @@ =head1 SYNOPSIS
     -mincn  	 -cn   Minimum CN change for copynumber_flag [0.3].
     -repeats   -r   Repeat file, see 'make-repeat-file' (legacy)
     -sampstat  -ss  ASCAT sample statistics file or file containing
-                      rho 0.XXXXX [0.75]
+                      rho 0.XXXXX [0.75] (~ 1-normalContamination)
                       Ploidy X.XXX [2.0]
                       GenderChr Y [Y]
-                      GenderChrFound Y\N
+                      GenderChrFound Y/N [Y]
     -platform  -pl  Sequencing platform (when not defined in BAM header)
     -tum_name  -tn  Tumour sample name (when not defined in BAM header)
     -norm_name -nn  Normal sample name (when not defined in BAM header)

diff --git a/perl/docs.tar.gz b/perl/docs.tar.gz
diff --git a/perl/lib/Bio/Brass.pm b/perl/lib/Bio/Brass.pm
@@ -1,7 +1,7 @@
 package Bio::Brass;
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2017 Genome Research Ltd.
 #
 # Author: Cancer Genome Project <cgpit@sanger.ac.uk>
 #
@@ -46,7 +46,7 @@ our @EXPORT = qw(find_breakpoints find_dusty_vertices
 		 is_dusty get_isolated_bp_alignment get_isolated_bp_surrounding_region
 		 $VERSION);
 
-our $VERSION = '5.3.0';
+our $VERSION = '5.3.1';
 
 =head1 NAME
 

diff --git a/perl/lib/Bio/Brass/Merge.pm b/perl/lib/Bio/Brass/Merge.pm
@@ -217,7 +217,7 @@ sub merge_headers {
   my $sample_counter = 0;
   for my $sample(@samples) {
     $sample_counter++;
-    $new_header .= sprintf "#SAMPLE\t%s\t%s\n", $sample_counter++, $sample;
+    $new_header .= sprintf "#SAMPLE\t%s\t%s\n", $sample_counter, $sample;
   }
   return $new_header;
 }

diff --git a/perl/lib/Sanger/CGP/Brass/Implement.pm b/perl/lib/Sanger/CGP/Brass/Implement.pm
@@ -748,8 +748,10 @@ sub _Rpath {
 
 sub get_ascat_summary {
   my ($options) = @_;
+  my $ret_val = 0;
   $options->{'PloidyAcfState'} = q{};
   if(defined $options->{'ascat_summary'}) {
+    $ret_val = 1;
     open my $SUMM, '<', $options->{'ascat_summary'};
     while(my $line = <$SUMM>) {
       chomp $line;
@@ -770,8 +772,11 @@ sub get_ascat_summary {
   if($options->{'PloidyAcfState'} ne 'REAL') {
     $options->{'Ploidy'} = 2;
     $options->{'Acf'} = 0.75;
-    $options->{'PloidyAcfState'} = 'DEFAULT'
+    $options->{'PloidyAcfState'} = 'DEFAULT';
+    $options->{'GenderChr'} = 'Y' unless(defined $options->{'GenderChr'});
+    $options->{'GenderChrFound'} = 'Y' unless(defined $options->{'GenderChrFound'});
   }
+  return $ret_val;
 }
 
 sub sanitised_sample_from_bam {