Modified mormal panel is now handled in more efficient way - makes BRASS GROUP step extremly faster

Merge branch 'release/v6.0.0'

Author: sb43

CHANGES.md

@@ -1,3 +1,7 @@
+
+### v6.0.0
+* Modified mormal panel is now handled in more efficient way - makes BRASS GROUP step extremly faster
+
 ### v5.4.1
 * Fix bug in implementation of cytoband option.
 

perl/MANIFEST

@@ -51,6 +51,7 @@ lib/Sanger/CGP/Rearrangement/Path.pm
 Makefile.PL
 MANIFEST			This list of files
 MANIFEST.SKIP
+perltidy.LOG
 share/Rdefaults/Human.GRCh37.CentTelo.tsv
 share/Rscripts/.Rhistory
 share/Rscripts/filter_small_deletions_and_fb_artefacts.R

perl/docs.tar.gz

@@ -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 = '5.4.1';
+our $VERSION = '6.0.0';
 
 =head1 NAME
 

perl/lib/Bio/Brass.pm

@@ -97,19 +97,16 @@ sub merge_records {
     if($n_grp) {
       # always clear the existing groups
       $n_grp->clear_group;
-
       # tabix BED now 1 based when queried
-      my $iter = $brass_np->query(sprintf '%s:%d-%d', $a_grp->low_chr, $a_grp->low_5p, $a_grp->low_3p);
+      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 %overlaps;
+      my $low_chr=$a_grp->low_chr;
       while(my $record = $iter->next){
+        $record=~s/^[^\t]+/$low_chr/; 
         $n_grp->new_group($record);
-        next if($a_grp->low_strand ne $n_grp->low_strand);
-        next if($a_grp->high_strand ne $n_grp->high_strand);
-        next if($a_grp->high_chr ne $n_grp->high_chr);
         next unless($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) {
         $n_grp->new_group($overlap);