You would replace

if (++$pos_count != $current[2]) {
            for my $pos ($pos_count .. $current[2]-1) {
                print join("\t", $current[1], $pos, '','', '1'), "\n";
            }
        }
[download]

with

        if (++$pos_count != $current[2]) {
            fill_interval($pos_count, @current);
        }
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where fill_interval() is defined as

sub fill_interval {
    my ($pos_count, @current) = @_;
    my $margin = 8;
    if ($current[2] - $pos_count <= 2*$margin) {
        for my $pos ($pos_count .. $current[2]-1) {
            print join("\t", $current[1], $pos, '','', '1'), "\n";
        }
    }
    else {
        my @bool;
        my ($start, $end) = ($pos_count, $current[2]-1);
        for my $i (0..$margin-1) {
            @bool[ $start + $i, $end - $i ] = (1,1);
        }
        
        for my $pos ($pos_count .. $current[2]-1) {
            print join("\t", $current[1], $pos, '','', $bool[$pos] || 
+0), "\n";
        }        
    }
}
[download]

Update: Changed literal values to $margin.