Commit 3cd178ba authored by Eugene Kulesha's avatar Eugene Kulesha
Browse files

it looks like the features overlapping origin can be attached to a normal...

it looks like the features overlapping origin can be attached to a normal slice as well as to an overlapping origin
parent 7d99cdd1
......@@ -288,10 +288,14 @@ my $seq = $slice->strand > 0 ? "$seq1$seq2" : "$seq2$seq1";
if ( $start > $end && $slice->is_circular() ) {
my ($seq, $seq1, $seq2);
my $midpoint = $slice->seq_region_length - $slice->start + 1;
$seq1 = ${ $self->_fetch_by_Slice_start_end_strand_circular( $slice, 1, $midpoint, 1 )};
$seq2 = ${ $self->_fetch_by_Slice_start_end_strand_circular( $slice, $midpoint + 1, $slice->length(), 1 )};
if ($slice->start < $slice->end) {
my $midpoint = $slice->seq_region_length - $slice->start + 1;
$seq1 = ${ $self->_fetch_by_Slice_start_end_strand_circular( $slice, 1, $midpoint, 1 )};
$seq2 = ${ $self->_fetch_by_Slice_start_end_strand_circular( $slice, $midpoint + 1, $slice->length(), 1 )};
} else {
$seq1 = ${ $self->_fetch_by_Slice_start_end_strand_circular( $slice, $slice->start, $slice->seq_region_length -1, 1 )};
$seq2 = ${ $self->_fetch_by_Slice_start_end_strand_circular( $slice, 1, $slice->end, 1 )};
}
$seq = $slice->strand > 0 ? "$seq1$seq2" : "$seq2$seq1";
reverse_comp( \$seq ) if ( $strand == -1 );
......
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