Mark DePristo 734756d6b2 Final fixes before BCF2 mark III push ... -- Added MLEAC and MLEAF format lines to PoolCallerWalker -- VariantFiltrationWalker now throws an error when JEXL variables cannot be found (XXX < 0.5) but passes through (albeit with a disgusting warning) when a variable is found but its value is a bad type (AF < 0.5) where AF == [0.04,0.00] at multi-allelic variation -- Allow values to pass assertEquals in VariantContextTestProvider when one file contains X=[null, null] and the other has X missing		2012-06-21 15:17:22 -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	Final fixes before BCF2 mark III push	2012-06-21 15:17:22 -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