Commit d02e36cf authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

Removed a bug in get_all_alt_locations for negative strand cases.

parent 4ffacb34
......@@ -1221,7 +1221,9 @@ sub seq {
=head2 get_all_alt_locations
Arg [1] : none
Arg [1] : Boolean override flag to force the method to return all
Features on the reference sequence as well.
Example : @features = @{$feature->get_all_alt_locations()};
foreach $f (@features) {
print $f->slice->seq_region_name,' ',$f->start, $f->end,"\n";
......@@ -1230,7 +1232,7 @@ sub seq {
Description: Retrieves shallow copies of this feature in its alternate
locations. A feature can be considered to have multiple
locations when it sits on a alternative structural haplotype
or when it is on a pseudo autosomal region. Most features will
or when it is on a Pseudo Autosomal Region. Most features will
just return a reference to an empty list though.
The features returned by this method will be on a slice which
covers the entire alternate region.
......@@ -1339,8 +1341,13 @@ sub get_all_alt_locations {
my $aslice = $axf->alternate_slice();
# position feature on entire slice of other region
$f->{'start'} = $f->seq_region_start() - $axf->start() + $aslice->start();
$f->{'end'} = $f->seq_region_end() - $axf->start() + $aslice->start();
# Cache seq_region_* to prevent contamination when changing feature coordinates.
my $seq_region_start = $f->seq_region_start();
my $seq_region_end = $f->seq_region_end();
$f->{'start'} = $seq_region_start - $axf->start() + $aslice->start();
$f->{'end'} = $seq_region_end - $axf->start() + $aslice->start();
$f->{'strand'} *= $aslice->strand();
$f->{'slice'} = $sa->fetch_by_seq_region_id($aslice->get_seq_region_id());
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