in reply to Loop through file to create interval tree

Please fix your formatting to make your code readable. Put one opening <code> at the beginning of the code, one closing </code> tag at the end of your code, and no <code> tag in the middle of your comments.

Otherwise, your splitting is very inefficient. You could get your 3 variables in just one operation:

while (my $line=<$fh>){ chomp $line; my ($low, $high, $id) = split /\t/, $line; # ...