gatk3的最后一个经典版本3.8

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
licensing	Remove old licensing	2012-04-25 12:23:08 -04:00
public	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
settings	Rev. tribble to fix BED codec bug in tribble 51	2012-01-17 16:40:26 -05:00
.gitignore	Minor additions to the shared .gitignore file, now that Mark has checked one in.	2011-10-26 12:24:28 -04:00
build.xml	Added function to get bases from the current base forward in the window in ReferenceContext	2012-04-06 16:07:46 -04:00
ivy.xml	Minor cleanup before push	2012-05-01 14:16:44 -04:00