gatk3的最后一个经典版本3.8

Christopher Hartl 365f1d2429 hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items: ... 1) ValidateVariants removed in favor of direct validation VariantContexts. Integration test added to test broken contexts. 2) Enabling indel and SV output. Still bi-allelic sites only. Integration tests added for these cases. 3) Found a bug where GQ recalculation (if a genotype has PLs but no GQ) would only happen for flipped encoding. Fixed. Integration test added.		2012-09-29 00:55:31 -04:00
licensing	Revert unintentional license change	2012-08-09 17:10:47 -04:00
protected/java	Fixed ReduceReads bug where variant regions were missing.	2012-09-19 16:09:08 -04:00
public	hmk123's error on the forum came from the reference context occasionally lacking bases needed for validating the reference bases in the variant context. (no @Window for VariantsToBinaryPed). This bugfix adresses this and other minor items:	2012-09-29 00:55:31 -04:00
settings	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00
.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	Convert external.build.dir and external.dist.dir back to paths	2012-08-15 23:04:10 -04:00
ivy.xml	Updating cofoja to the latest version	2012-08-09 16:36:18 -04:00