I am interested in checking if a SNP/position lies within a target region. These are the steps that I have in my script.
  1. Load target regions into a Hash of Array (chrN -> [coord1,coord2,coord3,...])
  2. Load SNP lines into an array
  3. Foreach SNP, if chrN key exists in the HOA, check if the coordN falls within a certain target region for each chromosome
  4. If yes, print the SNP line, else skip it
My script prints what I need, but is incredibly slow if there are say 10,000 lines or more in the input file.
Is there an quicker way to achieve the same?
I greatly appreciate any input in this regard!

In reply to What is the best approach to check if a position falls within a target range? by umasuresh

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