Mark DePristo 549293b6f7 Bugfixes towards final BCF2 implementation ... -- MLAC and MLAF in PoolCaller now use standard MLE_AC and MLE_AF -- VCFDiffableReader disables onTheFly fixing of VCF header fields so comparisons are easier when headers are changing -- Flag fields with FLAG_KEY=0 are parsed as though FLAG_KEY were entirely absent in AbstractVCFCodec to fix bug where FLAG_KEY=0 was being translated into FLAG_KEY in output VCF, making a false flag value a true one -- Fix the GT field value in VariantContextTestProviders so it isn't fixed 1000s of times during testing -- Keys whose value is null are put into the VariantContext info attributes now		2012-06-21 15:17:21 -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	Bugfixes towards final BCF2 implementation	2012-06-21 15:17:21 -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	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
testdata	Moved most testdata from public to private	2012-06-21 15:17:19 -04:00