Mark DePristo 567dba0f76 Cleanup of VCF header lines and constants, BCF2 bugfixes ... -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header		2012-06-21 15:16:31 -04:00
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datasources	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
downsampling	Make downsampler classes themselves generic (instead of just the Downsampler interface)	2012-06-13 16:43:39 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
iterators	Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.	2012-06-15 15:55:03 -04:00
refdata	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
report	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
samples	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
EngineFeaturesIntegrationTest.java	Nearing final BCF commit	2012-06-14 16:42:32 -04:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00