It looks to me as if - within each $window - you only need to count the occurrence of each of the 4 letters and then write a random sequence of those letters with the correct frequency of each. This only needs a bit of book keeping when reading and writing the files but should consume far less memory in the order of 4 times the number of windows.

But then I may not really have understood your shuffling requirements...

In reply to Re: Reduce RAM required by hdb
in thread Reduce RAM required by onlyIDleft

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