Mark DePristo aaf11f00e3 Near final BCF2 implementation ... -- Trivial import changes in some walkers -- SelectVariants has a new hidden mode to fully decode a VCF file -- DepthPerAlleleBySample (AD) changed to have not UNBOUNDED by A type, which is actually the right type -- GenotypeLikelihoods now implements List<Double> for convenience. The PL duality here is going to be removed in a subsequent commit -- BugFixes in BCF2Writer. Proper handling of padding. Bugfix for nFields for a field -- padAllele function in VariantContextUtils -- Much better tests for VariantContextTestProvider, including loading parts of dbSNP 135 and the Phase II 1000G call set with genotypes to test encoding / decoding of fields.		2012-05-24 10:57:02 -04:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each.	2012-05-21 15:41:56 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	Near final BCF2 implementation	2012-05-24 10:57:02 -04:00
BaseTest.java	Testing of BCF codec	2012-05-24 10:57:01 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00