Mark DePristo a648b5e65e First step towards an efficient Genotype object ... -- Created new clean FastGenotype and GenotypeBuilder classes with contracts to enforce expected behavior and correctness. Tested utility of this approach by rewritting -- and then commenting out -- a path in BCF2Codec that could use this new code. Much cleaner interface now, but not yet hooked up to anything -- Disabled SHADOW_BCF generation and generating contigs in the output VCFs automatically to ensure that the current code bases integration tests, before switching the code to new Genotype class -- Code cleanup. Moved "AD" to VCFConstants under GENOTYPE_ALLELIC_DEPTHS. Uses in code replaced with constant		2012-06-14 16:42:23 -04:00
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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	I hate these disabled unit tests, #2	2012-06-14 15:19:27 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Fixed comparison of VCFHeader as the set.equals() isn't working as expected	2012-06-14 16:42:22 -04:00
BaseTest.java	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
MD5DB.java	Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s	2012-05-28 20:20:05 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	First step towards an efficient Genotype object	2012-06-14 16:42:23 -04:00