NAME

Bio::Gonzales::Range::Overlap - find overlapping ranges

SYNOPSIS

use 5.010;
use Bio::Gonzales::Range::Overlap;
use Data::Dumper;

my @ranges1 = (
  [ 0, 5, 'some', 'information' ],
  [ 6, 8,  'some',     'other', 'information' ],
  [ 7, 10, 'nonsense', 'information' ],
  [ 11, 100, { 'very' => 'complicated', "data" => 'structure' } ],
);

my $ro = Bio::Gonzales::Range::Overlap->new;

#build query db from 1st set of intervals
for my $r (@ranges1) {
  $ro->insert(@$r);
}

# in this case (from and to are elements 0 and 1)
# insert could be called with all ranges
#$ro->insert(\@ranges1);

my @ranges2 = ( [ 8, 10 ], [ 1, 3 ], [99,200],);

# query the db with ranges
for my $r (@ranges2) {
  say "Range (" . join(",", @$r) . ") overlaps with:";
  say Dumper $ro->overlaps_with(@$r);
}

DESCRIPTION

A @range has the form ($from, $to, @additional elements). Lists of ranges have the form ([$from, $to, @add_elems], [$from, $to, @add_elems], ...).

OPTIONS

METHODS

$ro->insert(@range)

$ro->insert(\@list_of_ranges)

\@ranges_contained_in_given_range = $ro->contained_in(@range)

\@ranges_that_overlap_with_given_range = $ro->overlaps_with(@range)

SEE ALSO

Bio::Gonzales::Matrix::IO for reading in ranges from files

Bio::Gonzales::Range::GroupedOverlap for grouped ranges such as genes that are grouped by chromosomes.

AUTHOR

jw bargsten, <jwb at cpan dot org>