Fix buffer logic for multi-allelic variants

Author: likhitha-surapaneni

modules/Bio/EnsEMBL/VEP/InputBuffer.pm

@@ -191,9 +191,6 @@ sub next {
   while(@$pre_buffer && @$buffer < $buffer_size) {
     my $vf = $pre_buffer->[0];
 
-    ## Set minimal to 1 if indel
-    $self->{minimal} = 1 if (defined($vf->{minimised}) && $vf->{minimised});
-
     # new chromosome
     if($prev_chr && $vf->{chr} ne $prev_chr) {
       $self->split_variants() if $self->{minimal};
@@ -212,8 +209,6 @@ sub next {
   if(my $parser = $self->parser) {
     while(@$buffer < $buffer_size && (my $vf = $parser->next)) {
 
-      ## Set minimal to 1 if indel
-      $self->{minimal} = 1 if (defined($vf->{minimised}) && $vf->{minimised});
 
       # exit the program if the maximum number of variants not ordered in the input file is reached
       if (!$self->param('no_check_variants_order') &&
@@ -262,8 +257,7 @@ sub next {
     die($error_msg);
   }
 
-  $self->split_variants() if $self->{minimal};
-
+  $self->split_variants() if $self->{minimal}  ;
   return $buffer;
 }
 

modules/Bio/EnsEMBL/VEP/Parser.pm

@@ -858,8 +858,16 @@ sub post_process_vfs {
       # For VCF input, the allele_string is trimmed to remove anchor base, so we capture original allele
 
       my $original_allele_string = ($vf->{nontrimmed_allele_string} || $vf->{allele_string});
-      my ($ref_allele_string,$alt_allele_string) = split(/\//, $original_allele_string);
-      $is_non_minimised_indel = 1 unless length($ref_allele_string) == length($alt_allele_string) or $original_allele_string =~ /-/;
+      my @alleles = split(/\//, $original_allele_string);
+      my $ref_allele_string = shift @alleles;
+      my $alt_allele_count;
+
+      foreach my $alt(@alleles) {
+        if (length($ref_allele_string) != length($alt) or $original_allele_string =~ /^-/){
+          $is_non_minimised_indel = 1;
+          last;
+        }
+      }
       $vf = ${$self->minimise_alleles([$vf])}[0] if $is_non_minimised_indel;
     }
   }
@@ -961,6 +969,7 @@ sub minimise_alleles {
     {
       # Updating a flag to minimise multi-allelic variants in split_variants/rejoin_variants
       $vf->{minimised} = 1;
+      $vf->{original_allele_string} = $vf->{nontrimmed_allele_string} || $vf->{allele_string};
       push @return, $vf;
     }