Merge branch 'hotfix/v6.1.2'

Author: David Jones

.travis.yml

@@ -35,7 +35,7 @@ install:
  - ./setup.sh $HOME/wtsi-opt
  - cd ../
  - rm -rf cgpBigWig
- - git clone --depth 1 --single-branch --branch dev https://github.com/ICGC-TCGA-PanCancer/PCAP-core.git
+ - git clone --depth 1 --single-branch --branch develop https://github.com/cancerit/PCAP-core.git
  - cd PCAP-core
  - ./setup.sh $HOME/wtsi-opt
  - cd ../

CHANGES.md

@@ -1,5 +1,9 @@
 # Changes
 
+## v6.1.2
+
+* Change tabix->query to tabix->query_full
+
 ## v6.1.1
 
 * Reduce I/O for small cpu overhead in coverage step

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 = '6.1.1';
+our $VERSION = '6.1.2';
 
 =head1 NAME
 

perl/lib/Bio/Brass/Merge.pm

@@ -108,14 +108,16 @@ sub merge_records {
       # always clear the existing groups
       $n_grp->clear_group;
       # tabix BED now 1 based when queried
-      my $iter = $brass_np->query(sprintf '%s%s%s%s:%d-%d', $a_grp->low_chr, $a_grp->low_strand, $a_grp->high_chr, $a_grp->high_strand, $a_grp->low_5p, $a_grp->low_3p);
+      my $iter = $brass_np->query_full(sprintf('%s%s%s%s', $a_grp->low_chr, $a_grp->low_strand, $a_grp->high_chr, $a_grp->high_strand), $a_grp->low_5p, $a_grp->low_3p);
       my %overlaps;
       my $low_chr=$a_grp->low_chr;
-      while(my $record = $iter->next){
-        $record=~s/^[^\t]+/$low_chr/;
-        $n_grp->new_group($record);
-        next unless($a_grp->high_3p >= $n_grp->high_5p && $a_grp->high_5p <= $n_grp->high_3p);
-        $overlaps{"@{$n_grp->{_loc_data}}"} = $record;
+      if(defined($iter)){
+        while(my $record = $iter->next){
+          $record=~s/^[^\t]+/$low_chr/;
+          $n_grp->new_group($record);
+          next unless($a_grp->high_3p >= $n_grp->high_5p && $a_grp->high_5p <= $n_grp->high_3p);
+          $overlaps{"@{$n_grp->{_loc_data}}"} = $record;
+        }
       }
       my $overlap = filter_overlaps(\%overlaps, $n_grp->sample_count);
       if(defined $overlap) {