Mark DePristo 27e7e17dc7 New way to handle exceptions in multi-threaded GATK ... -- HMS no longer tries to grab and throw all exceptions. Exceptions are just thrown directly now. -- Proper error handling is handled by functions in HMS, which are used by ShardTraverser and TreeReducer -- Better printing of stack traces in WalkerTest		2012-04-13 09:23:33 -04:00
..
R	Now converts gatkreports to properly typed R data types in gsa.read.gatkreport	2012-03-02 09:11:59 -05:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	New way to handle exceptions in multi-threaded GATK	2012-04-13 09:23:33 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.	2012-02-22 17:20:04 -05:00
testdata	Added support for breakpoint alleles	2012-02-23 12:14:48 -05:00