Matt Hanna d170187896 Disable optimization that increases marginal speed of the GATK slightly but ... can produce data loss in a narrow corner case where the BGZF block(s) locations and offsets in the last index bucket of contig n overlap exactly with the BGZF block locations and offset in the last index bucket of contig n+1. A proper fix that keeps the optimization has already been introduced into unstable, but disabling the optimization is a low risk way to make sure that users of stable experience no data loss.		2011-08-17 16:16:05 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Disable optimization that increases marginal speed of the GATK slightly but	2011-08-17 16:16:05 -04:00
test	There are some really 'interesting' (but apparently valid) records in the Mus musculus dbSNP file. Generalized the handling of complex cases in the dbSNP adaptor to handle it all. I just grabbed the actual Mus musculus dbSNP file as a test, ran it whole genome, and confirmed that we finally produce a valid VCF on it. Should be the last commit needed on this adaptor.	2011-07-28 13:55:58 -04:00