Ryan Poplin c3b6e2b143 Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable		2012-08-03 13:14:43 -04:00
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src/org/broadinstitute/sting	Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-08-03 13:14:43 -04:00
test/org/broadinstitute/sting/gatk/walkers	Simple cleanup of pool caller code - since usage is much more general than just calling pools, AF calculation models and GL calculation models are renamed from Pool -> GeneralPloidy. Also, don't have users specify special arguments for -glm and -pnrm. Instead, when running UG with sample ploidy != 2, the correct general ploidy modules are automatically detected and loaded. -glm now reverts to old [SNP|INDEL|BOTH] usage	2012-07-31 16:34:20 -04:00