Hi Eily, thank you for the greeting, the compliment, and the debugging suggestions. I already like how you have defined the scalars, it is much cleaner and easier to read than my original. Unfortunately I will have to create an intermediate array as I will have several ref start/end/info values for a given chr/strand pair. I posted a sample of the reference file below with unnecessary information dotted out:

1       .  .    14404   14501   .       -       .       Name=DDX11
1       .  .    15005   15038   .       -       .       Name=ACTB

[download]

Cheers!

In reply to Re^2: How to make a hash to evaluate columns between large datasets by rambosauce
in thread How to make a hash to evaluate columns between large datasets by rambosauce

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