in reply to slurping many Arrays into memory...Please Help

If you explain what you are actually trying to do, it would be easier to check your code and tell you whether it is efficient or not. If all you try to do is to grep the files for the string "chr1:8325525" then there is no need to slurp all the data into memory first.

If you show a short example of one of the input files and of the result you expect, then we can perhaps suggest more improvements for your code.

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

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