Eric Banks 2f800b078c Changes to default behavior of UG: multi-allelic mode is always on; max number of alternate alleles to genotype is 3; alleles in the SNP model are ranked by their likelihood sum (Guillermo will do this for indels); SB is computed again.		2012-02-08 15:27:16 -05:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Changes to default behavior of UG: multi-allelic mode is always on; max number of alternate alleles to genotype is 3; alleles in the SNP model are ranked by their likelihood sum (Guillermo will do this for indels); SB is computed again.	2012-02-08 15:27:16 -05:00