Solved major scalability problem in pool caller - exact model may have been linear but computing pool GL's was O(n^p) where p was max # of alleles (4 in SNP discovery mode). Linearized approach follows exact AF model with queue of AC conformations to add - may refactor code to eliminate duplication later, as linear multiallelic pool AF model will use same approach. TBD: how to print PL's with -Infinity value, right now since we never cap PL printing we end up with big nonsense numbers in those positions and vcf's look ugly. Calling MT in CEU trio with pool size = 100 goes from 2 days to 55 minutes (sic)

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Guillermo del Angel 2012-05-11 10:05:09 -04:00

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commit 67e5c3ff9f

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