Merge branch 'release/v2.1.2'

Update to remove depandancy on custom algorithm specific VCF INFO tags to parse indel data, uses basic VCF spec fields instead.

MYMETA.json

@@ -53,5 +53,5 @@
       }
    },
    "release_status" : "stable",
-   "version" : "v2.1.1"
+   "version" : "v2.1.2"
 }

MYMETA.yml

@@ -35,4 +35,4 @@ requires:
   Sort::Key: 1.33
   TAP::Harness: 3.33
   Try::Tiny: 0.22
-version: v2.1.1
+version: v2.1.2

bin/AnnotateVcf.pl

@@ -288,7 +288,7 @@ sub parse_vcf_record {
   # a straight deletion
   if($ref_len > 1 && $alt_len == 1) {
     my $min = $pos + 1; # as vcf records base before for non-insert
-    my $max = $min + ($vcf->get_info_field($record->[$INFO_COL], 'LEN') - 1);
+    my $max = $min + ($ref_len - 2); # ref_len contains both the start base and the extra anchor base, have to deduct 2
     $var = Sanger::CGP::Vagrent::Data::Deletion->new(
 							'species'				=> $opts->{'species'},
 							'genomeVersion' => $opts->{'assembly'},
@@ -321,7 +321,7 @@ sub parse_vcf_record {
   # complex indel
   elsif($ref_len > 1 && $alt_len > 1) {
     my $min = $pos + 1; # as vcf records base before for non-insert
-    my $max = $min + ($vcf->get_info_field($record->[$INFO_COL], 'LEN') - 1);
+    my $max = $min + ($ref_len - 2); # ref_len contains both the start base and the extra anchor base, have to deduct 2
     $var = Sanger::CGP::Vagrent::Data::ComplexIndel->new(
 							'species'				=> $opts->{'species'},
 							'genomeVersion' => $opts->{'assembly'},

lib/Sanger/CGP/Vagrent.pm

@@ -26,7 +26,7 @@ use strict;
 use Const::Fast qw(const);
 
 use base 'Exporter';
-our $VERSION = '2.1.1';
+our $VERSION = '2.1.2';
 our @EXPORT = qw($VERSION);
 
 1;