Mark DePristo 5b0ade67c8 Updates to VCF processing for better BCF processing ... -- getMetaData now split into getMetaDataInSortedOrder() [old functionality] and getMetaDataInOriginalOrder() [according to the header order]. Important as BCF uses the order of elements in the header in the offsets to keys, and we were automatically sorting the BCF2 header which is out of order in samtools and the whole system was going crazy -- Updating GATK code to use the appropriate header function (this is why so many files have changed) -- BCF2 code was busted in not differentiating PASS from . from FILTER in VC (tests coming that will actually stress this) -- Bugfix for adding contig lines to BCF2 header dictionary -- VCFHeader metaData no longer sorted internally. The system now maintains the data in header order, and only sorts output as requested in API -- VCFWriter and BCF2Writer now explictly sort their header lines -- Don't allow filters to be added that are PASS in the contract		2012-07-08 15:44:33 -07:00
..
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	…
doc	…
java	Updates to VCF processing for better BCF processing	2012-07-08 15:44:33 -07:00
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	Pass the original GATK unsafe parameter to the VcfGatherFunction	2012-07-02 16:03:11 -04:00
testdata	Changing the logic of the -standard argument; the way it stands currently one can never turn off the cycle or context covariates. Now they are on by default and users must opt out of them to turn them off.	2012-07-04 00:21:21 -04:00