gatk3的最后一个经典版本3.8

Mark DePristo 3144eae51c UnifiedGenotyper bugfix: don't create haplotypes with 0 bases ... -- The PairHMM no longer allows us to create haplotypes with 0 bases. The UG indel caller used to create such haplotypes. Now we assign -Double.MAX_VALUE likelihoods to such haplotypes. -- Add integration test to cover this case, along with private/testdata BAM -- [Fixes #47523579]		2013-04-13 14:57:55 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	UnifiedGenotyper bugfix: don't create haplotypes with 0 bases	2013-04-13 14:57:55 -04:00
public	Several improvements to ReadAdaptorTrimmer so that it can be incorporated into ancient DNA processing pipelines (for which it was developed):	2013-04-13 13:41:36 -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	Disable Contracts for Java for tests	2013-04-04 11:56:17 -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