Mark DePristo 31997f8092 Bugfixes on the way to passing integration tests ... -- Replaced getAttributes with getDP() and not the old style getAttribute, where appropriate -- Added getAnyAttribute and hasAnyAttribute that actually does the expensive work of seeing if the key is something like GT, AD or another inline datum, and returns it. Very expensive but convenient. -- Fixed nasty subsetting bug in SelectVariants with excluding samples -- Generalized VariantsToTable to work with new inline attributes (using getAnyAttribute) as well as GT -- Bugfix for dropping old style GL field values -- Added test to VCFWriter to ensure that we have the sample number of samples in the VC as in the header -- Bugfix for Allele.getBaseString to properly show NO_CALL alleles -- getGenotypeString in Genotype returns "NA" instead of null for ploidy == 0 genotypes		2012-06-14 16:42:33 -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	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
gatk	Bugfixes on the way to passing integration tests	2012-06-14 16:42:33 -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	Genotype encoding uses the BCF2FieldEncoder system	2012-06-14 16:42:33 -04:00
BaseTest.java	Initial version of clean, fast formatting routines built dynamically from a VCF header	2012-06-14 16:42:30 -04:00
MD5DB.java	Algorithmically faster version of DiffEngine	2012-06-14 16:42:30 -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	Initial version of clean, fast formatting routines built dynamically from a VCF header	2012-06-14 16:42:30 -04:00