view release on metacpan or  search on metacpan

lib/App/Rangeops/Command/clean.pm  view on Meta::CPAN

            $info_of->{$r0}{chr} eq $info_of->{$r1}{chr} ? ($_) : ()
        } @lines;

        for my $line (@same_pair_lines) {
            my ( $range0, $range1 ) = split /\t/, $line;

            my $intspan0 = $info_of->{$range0}{intspan};
            my $intspan1 = $info_of->{$range1}{intspan};

            my $intspan_i = $intspan0->intersect($intspan1);
            if ( $intspan_i->is_not_empty ) {
                if (    $intspan_i->size / $intspan0->size > 0.5
                    and $intspan_i->size / $intspan1->size > 0.5 )
                {
                    @lines = grep { $_ ne $line } @lines;
                }
            }
        }
    }

    #----------------------------#

lib/App/Rangeops/Command/merge.pm  view on Meta::CPAN

            my $range_i = $ranges[$i];
            printf STDERR " " x 4 . "Range %d / %d\t%s\n", $i, $#ranges,
                $range_i
                if $opt->{verbose};
            my $set_i = $info_of->{$range_i}{intspan};
            for my $j ( $i + 1 .. $#ranges ) {
                my $range_j = $ranges[$j];
                my $set_j   = $info_of->{$range_j}{intspan};

                my $i_set = $set_i->intersect($set_j);
                if ( $i_set->is_not_empty ) {
                    my $coverage_i = $i_set->size / $set_i->size;
                    my $coverage_j = $i_set->size / $set_j->size;
                    if (    $coverage_i >= $opt->{coverage}
                        and $coverage_j >= $opt->{coverage} )
                    {
                        push @edges, [ $ranges[$i], $ranges[$j] ];
                        printf STDERR " " x 8
                            . "Merge with Range %d / %d\t%s\n",
                            $j, $#ranges, $range_j
                            if $opt->{verbose};