Commit 3eb40c77 authored by William McLaren's avatar William McLaren
Browse files

Include read coverage filtering for sequence

parent 72fcd640
......@@ -535,7 +535,10 @@ sub seq {
# get slice/mapper pairs from mapped slice (usually only one anyway)
foreach my $pair(@{$self->get_all_Slice_Mapper_pairs()}) {
my ($s, $m) = @$pair;
my $seq = $s->seq();
# make sure to send extra args
# eg strain slices might need read coverage filtering
my $seq = $s->seq(@_);
# project from mapped slice to reference slice using the mapper
foreach my $ref_coord($m->map_coordinates('mapped_slice', 1, CORE::length($seq), $s->strand, 'mapped_slice')) {
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