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sub merge {
  my ($pre,$cur,$nex, $mindist) = @_;
...
  my $decicion_to_merge = ...
  if( $decicion_to_merge == 1 ){ ... merge the intervals ... }
}

sub     get_sorted_intervals_as_array {
        my $atree = shift;
...
        );
        return @ret
}

my @ints = get_sorted_intervals_as_array($tree);
for($i=1;$i<scalar(@ints)-1;$i++){
...
   $nex = $ints[$i+1];
   merge($pre, $cur, $nex, 1234); # 1234 user-specified distance
}

my %Interval  = (
   'chromosome' => 'Chr1',
...
   'type' => 'A',
   'id' => 1
);

sub can_merge {
  my ($i1, $i2) = @_;
...
  ...
  return $newi # return the new interval representing the merge
}