Guillermo del Angel 605984353f Pool Caller improvements: a) New non-standard private annotation Heteroplasmy which measures mean heteroplasmy (pool AF) across called samples, meant for easier mtDNA calling. Pure homoplasmic variants (pool AF = 1 or 0) would have heteroplasmy=1. b) Don't output pool genotypes by default for large pool sizes because it makes file sizes explode and they're unreadable. c) Refactored classes ExactACCounts and ExactACSet and moved to superclass AlleleFrequencyCalculationModel because both Pool and Exact AF calculation models will use it. d) Initial refactorings and skeleton for linearized multi-allelic exact model (not done yet). e) Unit test for Pool AF calculation model.		2012-05-08 09:33:38 -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	Pool Caller improvements: a) New non-standard private annotation Heteroplasmy which measures mean heteroplasmy (pool AF) across called samples, meant for easier mtDNA calling. Pure homoplasmic variants (pool AF = 1 or 0) would have heteroplasmy=1. b) Don't output pool genotypes by default for large pool sizes because it makes file sizes explode and they're unreadable. c) Refactored classes ExactACCounts and ExactACSet and moved to superclass AlleleFrequencyCalculationModel because both Pool and Exact AF calculation models will use it. d) Initial refactorings and skeleton for linearized multi-allelic exact model (not done yet). e) Unit test for Pool AF calculation model.	2012-05-08 09:33:38 -04:00
test	As promised in the release notes for 1.6, I am removing the old deprecated genotyping framework revolving around the misordering of alleles and have moved the fixed version in its place in preparation for release 1.7 (or 2.0?).	2012-05-01 16:18:24 -04:00