Merge pull request #130 from ens-lgil/release/91

Fix missing ';' character when the INFO column of the input VCF conta…
Ensembl · Jan 24, 2018 · b70ec49 · b70ec49
2 parents 461fc6e + 0ca9972
commit b70ec49
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/Constants.pm b/modules/Bio/EnsEMBL/VEP/Constants.pm
@@ -53,7 +53,7 @@ use warnings;
 use base qw(Exporter);
 
 our $VEP_VERSION     = 91;
-our $VEP_SUB_VERSION = 1;
+our $VEP_SUB_VERSION = 2;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm b/modules/Bio/EnsEMBL/VEP/OutputFactory/VCF.pm
@@ -275,7 +275,8 @@ sub get_all_lines_by_InputBuffer {
 
       # nuke existing CSQ field?
       if($line->[7] =~ /(^|\;)$fieldname\=/ && !$self->{keep_csq}) {
-        $line->[7] =~ s/(^|\;)$fieldname\=\S+?(\;|$)(\S|$)/$3/;
+        $line->[7] =~ s/(^|\;)$fieldname\=\S+?(\;\S|$)/$2/;
+        $line->[7] =~ s/^\;//;
       }
     }
 
@@ -471,4 +472,4 @@ sub web_output_fh {
   return $self->{_web_output_fh};
 }
 
-1;
+1;