Mark DePristo 1f45551a15 Bugfixes to G count types in VCF header ... -- Previously VCF header lines of count type G assumed that the sample would be diploid. -- Generalized the code to take a VariantContext and return the right result for G count types by calling into the correct numGenotypes in GenotypeLikelihoods class -- renamed calcNumGenotypes to numGenotypes, which uses a static cache in the class -- calcNumGenotypes is private, and is used to build the static cache or to compute on the fly for uncached No. allele / ploidy combinations -- VariantContext calls into getMaxPloidy in GenotypesContext, which caches the max ploidy among samples -- Added extensive unit tests that compare A and G type values in genotypes		2012-06-26 15:28:34 -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	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
gatk	VariantRecalibrator test currently doesn't work with shadowBCF	2012-06-26 15:28:34 -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	Bugfixes to G count types in VCF header	2012-06-26 15:28:34 -04:00
BaseTest.java	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
MD5DB.java	Finalizing BCF2 mark III commit	2012-06-21 15:16:27 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	…
WalkerTest.java	Disable shadowBCF for VariantRecalibrationWalkers tests because it cannot handle symbolic alleles yet	2012-06-26 15:28:32 -04:00