Merge branch 'hotfix/v6.3.2'

Author: keiranmraine

CHANGES.md

@@ -1,5 +1,10 @@
 # Changes
 
+## v6.3.2
+
+* Fix edgecase on RG line handling (#99)
+* Ensure attempt to run on completion give exit==0 (#98)
+
 ## v6.3.1
 
 * Handle undefined value edge case #95.

Dockerfile

@@ -69,7 +69,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="v6.2.2" \
+      version="v6.3.2" \
       description="BRASS docker"
 
 RUN apt-get -yq update \

perl/bin/brass.pl

@@ -298,7 +298,7 @@ sub setup {
   my $final_logs = File::Spec->catdir($opts{'outdir'}, 'logs');
   if(-e $intermediates && -e $final_logs) {
     warn "NOTE: Presence of intermediates.tar.gz and final logs directories suggests successful complete analysis, please delete to proceed: $intermediates\n";
-    exit 1;
+    exit 0; # don't cause failure
   }
 
   # now safe to apply defaults

perl/bin/brassI_prep_bam.pl

@@ -141,6 +141,7 @@ sub process_header {
     $count_in_bam++;
     my $rg_id = 0;
     $rg_id = $1 if($row =~ /\tID:([^\t]+)/);
+    chomp $rg_id;
 
     # die horribly if RG ids don't match
     unless (defined $bas_ob->get($rg_id, 'readgroup')) { die "Readgroup $rg_id in bam file but not in bas file $!"; }

perl/lib/Bio/Brass.pm

@@ -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 = '6.3.1';
+our $VERSION = '6.3.2';
 
 =head1 NAME