gatk3的最后一个经典版本3.8

Mark DePristo d7bec9eb6e AssessNA12878 bugfixes ... -- @Output isn't required for AssessNA12878 -- Previous version would could non-variant sites in NA12878 that resulted from subsetting a multi-sample VC to NA12878 as CALLED_BUT_NOT_IN_DB sites. Now they are properly skipped -- Bugfix for subsetting samples to NA12878. Previous version wouldn't trim the alleles when subsetting down a multi-sample VCF, so we'd have false FN/FP sites at indels when the multi-sample VCF has alleles that result in the subset for NA12878 having non-trimmed alleles. Fixed and unit tested now.		2013-03-18 15:48:08 -04:00
licensing	Removing the symlink from the private license file	2013-02-09 12:57:44 -05:00
protected	Bug fix in assembly for edge case in which the extendPartialHaplotype function was filling in deletions in the middle of haplotypes.	2013-03-15 14:20:25 -04:00
public	AssessNA12878 bugfixes	2013-03-18 15:48:08 -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