gatk3的最后一个经典版本3.8

Guillermo del Angel 596c1723ae Hidden, unsupported ability of VariantEval to run AlleleCount stratification on sites-only VCFs. I'll expose it/add tests on it if people think this is generaly useful. User needs to specify total # of samples as command line argument since genotypes are not available. ... Also, fixes to large-scale validation script: lower -minIndelFrac threshold or else we'll kill most indels since default 0.25 is too high for pools, fix also VE stratifications and add one VE run where eval=1KG, comp=pool data and AC stratification based on 1KG annotation		2012-10-25 10:35:43 -04:00
licensing	Final final final version of the license.	2012-07-20 18:00:02 -04:00
protected/java	MaxAltAlleles now defaults to 6, no more MaxAltAllelesForIndels	2012-10-22 13:47:56 -04:00
public	Hidden, unsupported ability of VariantEval to run AlleleCount stratification on sites-only VCFs. I'll expose it/add tests on it if people think this is generaly useful. User needs to specify total # of samples as command line argument since genotypes are not available.	2012-10-25 10:35:43 -04:00
settings	Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component.	2012-10-16 02:22:30 -04:00
.gitignore	adding some directories to gitignore	2012-09-27 11:09:41 -04:00
build.xml	Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component.	2012-10-16 02:22:30 -04:00
intellij_example.tar.bz2	Removed the intellij files from the root and made an example package for new users. This allows users to start at the same page and then change it as they see fit without interfering with the repo (thanks guillermo!)	2012-09-27 11:04:56 -04:00
ivy.xml	Updated google reflections due to stale slf4j version conflicting with other projects also trying to use Queue as a component.	2012-10-16 02:22:30 -04:00