gatk3的最后一个经典版本3.8

Guillermo del Angel ea01dbf130 Fix to issue encountered when running HaplotypeCaller in GGA mode with data from other 1000G callers. ... In particular, someone produced a tandem repeat site with 57 alt alleles (sic) which made the caller blow up. Inelegant fix is to detect if # of alleles is > our max cached capacity, and if so, emit an informative warning and skip site. -- Added unit test to UG engine to cover this case. -- Commit to posterity private scala script currently used for 1000G indel consensus (still very much subject to changes). GSA-878 #resolve		2013-03-20 14:30:37 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Fix to issue encountered when running HaplotypeCaller in GGA mode with data from other 1000G callers.	2013-03-20 14:30:37 -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