gatk3的最后一个经典版本3.8

Mark DePristo df90597bfc Performance optimizations and caliper benchmarking code for consolidateCigar ... -- Now that this function is used in the core of LIBS it needed some basic optimizations, which are now complete, pass all unit tests. -- Added caliper benchmark for AlignmentUtils to assess performance (showing new version is 3x-10x faster) -- Remove unused import in ReadStateManager		2013-04-24 11:36:43 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Corner case fix to General Ploidy SNP likelihood model.	2013-04-23 21:13:18 -04:00
public	Performance optimizations and caliper benchmarking code for consolidateCigar	2013-04-24 11:36:43 -04:00
settings	Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec).	2013-04-05 00:52:32 -04:00
.gitignore	Fixing the licensing scripts	2013-01-26 13:42:49 -05:00
build.xml	Add additional necessary class files to na12878kb.jar target	2013-04-23 14:03:48 -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	Brought all of ReduceReads to fastutils	2013-02-23 22:53:23 -05:00