if ( $ref eq '*' )
{
# An indel is involved.
- if ( $ignore_indels ) { next; }
+ if ( $ignore_indels )
+ {
+ $prev_ref = $ref;
+ $prev_pos = $pos;
+ $prev_chr = $chr;
+ next;
+ }
if (!defined $prev_chr || $chr ne $prev_chr || $pos ne $prev_pos)
{
}
else
{
- if ( $ignore_snps ) { next; }
+ if ( $ignore_snps )
+ {
+ $prev_ref = $ref;
+ $prev_pos = $pos;
+ $prev_chr = $chr;
+ next;
+ }
# SNP
($alt,$gt) = iupac_to_gtype($ref,$cons);