perf: speed up TRRecord.GetLengthGenotypes()
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use broadcasting to improve the speed as we scale up the number of samples
aryarm
changed the title
TRRecord.GetLengthGenotypes()TRRecord.GetLengthGenotypes()
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@LiterallyUniqueLogin, can I request a review from you since you were the original author of this code? What do you think of these changes? |
aryarm
changed the title
TRRecord.GetLengthGenotypes()TRRecord.GetLengthGenotypes()
aryarm
changed the title
TRRecord.GetLengthGenotypes()TRRecord.GetLengthGenotypes()
LiterallyUniqueLogin
approved these changes
Dec 21, 2023
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I was playing around with
GetLengthGenotypeswhen trying to integrate it into haptools and noticed there might be a potentially faster way of implementing it.This implementation vectorizes the for-loop using broadcasting, improving the speed as we scale up 1) the number of samples and 2) the number of alleles in each TR of a VCF. I benchmarked haptools for 1 (but not 2) via our benchmarking script (with some small adaptations).
I didn't add any tests to this PR because it's just a refactor.
GetLengthGenotypesalready has tests and they all seemed to pass with this new code. But feel free to let me know if there are any tests that it would be good for me to add.