gatk3的最后一个经典版本3.8

Mark DePristo a783f19ab1 Fix for potential HaplotypeCaller bug in annotation ordering ... -- Annotations were being called on VariantContext that might needed to be trimmed. Simply inverted the order of operations so trimming occurs before the annotations are added. -- Minor cleanup of call to PairHMM in LikelihoodCalculationEngine		2013-03-20 22:54:35 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Fix for potential HaplotypeCaller bug in annotation ordering	2013-03-20 22:54:35 -04:00
public	Created new DeprecatedToolChecks class	2013-03-20 06:46:02 -04:00
settings	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Fix tests that were consistently or intermittently failing when run in parallel on the farm	2013-03-06 13:56:54 -05:00
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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00