Merge pull request #538 from aparton/bugfix/rsIDsorting97

Prevent sorting check for list of rsIDs
Ensembl · Jul 23, 2019 · 306e3f4 · 306e3f4
2 parents 9a2d6bf + 507e55a
commit 306e3f4
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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     = 97;
-our $VEP_SUB_VERSION = 1;
+our $VEP_SUB_VERSION = 2;
 
 our @EXPORT_OK = qw(
   @FLAG_FIELDS

diff --git a/modules/Bio/EnsEMBL/VEP/InputBuffer.pm b/modules/Bio/EnsEMBL/VEP/InputBuffer.pm
@@ -234,7 +234,7 @@ sub next {
       else {
         push @$buffer, $vf;
         $prev_chr = $vf->{chr};
-        if (!$self->param('no_check_variants_order')) {
+        if (!$self->param('no_check_variants_order') && $self->param('format') ne 'id') {
           # Use a default distance to check if the variant is still in the same region
           # even if it's not ordered with the previous variant location: we use the VF start and not the VCF start
           # (they can be different when the variant is a deletion for instance and/or when the alleles can be minimised)