my ($self, $pair) = @_;
my $feature1 = $pair->feature1;
my $feature2 = $pair->feature2;
-seqname => $feature1->seq_id,
-start => $feature1->start,
-end => $feature1->end,
-strand => $feature1->strand,
-source_tag => $feature1->source_tag,
);
my ($h_start, $h_end);
if($feature1->strand == 1){
$h_start = $feature2->start;
$h_end = $feature2->end;
}elsif($feature1->strand == -1){
$h_start = $feature2->end;
$h_end = $feature2->start;
}else{
$self->throw("strand cannot be outside of (1, -1)");
}
$ens_repeatfeature->hstart($h_start);
$ens_repeatfeature->hend($h_end);
my $repeat_name = $feature2->seq_id;
my $repeat_class = $feature1->primary_tag;
$repeat_class ||= $feature2->primary_tag;
$repeat_class ||= "not sure";
my $ens_repeat_consensus =
$self->_create_consensus($repeat_name, $repeat_class);
$ens_repeatfeature->repeat_consensus($ens_repeat_consensus);
my($contig) = ref ($self->contig) eq 'ARRAY' ? @{$self->contig} : $self->contig;
$ens_repeatfeature->attach_seq($contig);
$ens_repeatfeature->analysis($self->analysis);
return $ens_repeatfeature;
}