might help to see some of what the input file looks like. I have a feeling this line is wrong:

if ($chrom[$i] =~ /chrd+/) {

unless you really are looking for "chr" followed by one or more "d". Probably should be:

if ($chrom[$i] =~ /chr\d+/) {

in which case its searching for "chr" followed by one or more digits.

Use the perl highlighter to post perl code. The php highlighter will mangle some perl code.

Besides that, I also don't understand what you are wanting to do.