Mark DePristo 7506994d09 Nearing final BCF commit ... -- Cleanup some (but not all) VCF3 files. Turns out there are lots so... -- Refactored gneotype parser from VCFCodec and VCF3Codec into a single shared version in AbstractVCFCodec. Now VCF3 properly handles the new GenotypeBuilder interface -- Misc. bugfixes in GenotypeBuilder		2012-06-14 16:42:32 -04:00
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R	Bugfix for R 2.15 not including reshape	2012-06-14 16:42:29 -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	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Temporary fake release directories for Bamboo testing purposes	2012-05-31 16:04:07 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	MD5DB for integrationtest management now writes out a md5mismatches files for clean analysis	2012-06-14 16:42:27 -04:00
testdata	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -04:00