Merge branch 'hotfix/2.2.2'

cancerit · Mar 26, 2018 · dab56a8 · dab56a8
2 parents 1535249 + cea880e
commit dab56a8
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Showing 3 changed files with 13 additions and 14 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 2.2.2
+
+* Change tabix query call to query_full
+
 ## 2.2.1
 
 * Handle files not being written by tophat-fusion-post when no events generated.

diff --git a/perl/bin/compare_CN_and_fusion.pl b/perl/bin/compare_CN_and_fusion.pl
@@ -114,12 +114,14 @@ sub get_start_end {
 sub search_break_point_annotations {
  my($chr,$start,$end,$tabix,$transcript1,$transcript2,$fusion_line)=@_;
 	my $results=undef;
-  my $iter = $tabix->query(sprintf '%s:%d-%d', $chr,$start,$end);
-  while(my $record = $iter->next){
-    my ($lgene,$rgene)=(split "/", (split "\t",$record)[12]);
-    my($matched)=compare_transcripts($transcript1,$transcript2,$lgene,$rgene);
-    push(@$results,"$matched\t$fusion_line\t$record\n") if($matched );
-  }
+  my $iter = $tabix->query_full($chr,$start,$end);
+	if(defined($iter)){
+	  while(my $record = $iter->next){
+	    my ($lgene,$rgene)=(split "/", (split "\t",$record)[12]);
+	    my($matched)=compare_transcripts($transcript1,$transcript2,$lgene,$rgene);
+	    push(@$results,"$matched\t$fusion_line\t$record\n") if($matched );
+	  }
+	}
 return $results;
 }
 
@@ -146,10 +148,3 @@ sub compare_gene {
  	}
 	return $matched;
 }
-
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diff --git a/perl/lib/Sanger/CGP/CgpRna.pm b/perl/lib/Sanger/CGP/CgpRna.pm
@@ -36,7 +36,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '2.2.1';
+our $VERSION = '2.2.2';
 our @EXPORT = qw($VERSION);
 
 1;