Merge branch 'hotfix/v3.3.3'

cancerit · Apr 9, 2018 · aa224ec · aa224ec
2 parents 9fb12f9 + 238ba1b
commit aa224ec
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Showing 4 changed files with 8 additions and 2 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.3.3
+
+* fixing issue in Admin_CacheFileBuilder.pl where it would fail without the optional fai file 
+
 ## 3.3.2
 
 * Actually get the new `htslib` and `samtools` links correct in `setup.sh`

diff --git a/bin/Admin_CacheFileBuilder.pl b/bin/Admin_CacheFileBuilder.pl
@@ -620,7 +620,9 @@ sub featureOrderSortFunction {
 sub checkChromosome {
   my ($chr,$chrList) = @_;
   my $use_chr = undef;
-  if(first { $_ eq $chr } @$chrList){
+  if(!defined $chrList){
+    $use_chr = $chr;
+  } elsif (first { $_ eq $chr } @$chrList){
     $use_chr = $chr;
   } else {
     # chromosome not in fai file

diff --git a/docs.tar.gz b/docs.tar.gz
diff --git a/lib/Sanger/CGP/Vagrent.pm b/lib/Sanger/CGP/Vagrent.pm
@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '3.3.2';
+our $VERSION = '3.3.3';
 our @EXPORT = qw($VERSION);
 
 1;