Merge tag 'v4.2.1' into dev

* Update tabix call to use query_full
cancerit · Mar 26, 2018 · 392ceba · 392ceba
2 parents 809aaf2 + 79dab0c
commit 392ceba
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diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # Changes
 
+## 4.2.1
+
+* Update tabix call to use query_full
+
 ## 4.2.0
 
 * Upgrade to core R [ASCAT v2.5.1](https://github.com/Crick-CancerGenomics/ascat/releases/tag/v2.5)

diff --git a/perl/bin/utilities/ascatSnpPanelGenerator.pl b/perl/bin/utilities/ascatSnpPanelGenerator.pl
@@ -154,11 +154,13 @@ sub get_regions {
   for my $t_range(@top_ranges) {
     my ($c_chr, $c_start, $c_end) = @{$t_range};
     if(defined $exclude) {
-      my $iter = $exclude->query(sprintf "%s:%d-%d", $c_chr, $c_start, $c_end);
-      while(my $record = $iter->next){
-        my ($start0, $end1) = (split /\t/, $record)[1..2];
-        push @refined_regions, [sprintf("%s:%d-%d", $c_chr, $c_start, $start0), $c_chr, $c_start, $start0] unless($start0 == 0);
-        $c_start = $end1;
+      my $iter = $exclude->query_full($c_chr, $c_start, $c_end);
+      if(defined($iter)){
+        while(my $record = $iter->next){
+          my ($start0, $end1) = (split /\t/, $record)[1..2];
+          push @refined_regions, [sprintf("%s:%d-%d", $c_chr, $c_start, $start0), $c_chr, $c_start, $start0] unless($start0 == 0);
+          $c_start = $end1;
+        }
       }
     }
     push @refined_regions, [sprintf("%s:%d-%d", $c_chr, $c_start, $c_end), $c_chr, $c_start, $c_end];

diff --git a/perl/lib/Sanger/CGP/Ascat.pm b/perl/lib/Sanger/CGP/Ascat.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '4.2.0';
+our $VERSION = '4.2.1';
 our @EXPORT = qw($VERSION);
 
 const my $LICENSE =>