Mark DePristo 3afbc50511 More BCF2 improvements ... -- Refactored setting of contigs from VCFWriterStub to VCFUtils. Necessary for proper BCF working -- Added VCFContigHeaderLine that manages the order for sorting, so we now emit contigs in the proper order. -- Cleaned up VCFHeader operations -- BCF now uses the right header files correctly when encoding / decoding contigs -- Clean up unused tools -- Refactored header parsing routines to make them more accessible -- More minor header changes from Intellij		2012-05-24 10:56:52 -04:00
..
R	Add warning message about ratios in variantQCreport, give ratio for MAF > 10%	2012-04-25 12:22:32 -04:00
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	More BCF2 improvements	2012-05-24 10:56:52 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	build system overhaul	2012-05-17 15:16:29 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Minor updates to pacbio data processing script to make it work with the latest bwa version/settings.	2012-05-22 10:24:45 -04:00
testdata	Extensive refactoring of the GATKReports. This was a beast.	2012-05-18 01:11:26 -04:00