Mark DePristo 5b0ade67c8 Updates to VCF processing for better BCF processing ... -- getMetaData now split into getMetaDataInSortedOrder() [old functionality] and getMetaDataInOriginalOrder() [according to the header order]. Important as BCF uses the order of elements in the header in the offsets to keys, and we were automatically sorting the BCF2 header which is out of order in samtools and the whole system was going crazy -- Updating GATK code to use the appropriate header function (this is why so many files have changed) -- BCF2 code was busted in not differentiating PASS from . from FILTER in VC (tests coming that will actually stress this) -- Bugfix for adding contig lines to BCF2 header dictionary -- VCFHeader metaData no longer sorted internally. The system now maintains the data in header order, and only sorts output as requested in API -- VCFWriter and BCF2Writer now explictly sort their header lines -- Don't allow filters to be added that are PASS in the contract		2012-07-08 15:44:33 -07:00
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writer	Updates to VCF processing for better BCF processing	2012-07-08 15:44:33 -07:00
AlleleUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenotypeLikelihoodsUnitTest.java	Bugfixes to G count types in VCF header	2012-06-26 15:28:34 -04:00
GenotypeUnitTest.java	Genotype filters are now just Strings, not Set<String>	2012-06-30 11:22:47 -04:00
GenotypesContextUnitTest.java	Efficient Genotype object Intermediate commit	2012-06-14 16:42:24 -04:00
VCFJarClassLoadingUnitTest.java	Don't try to share BCF2 yet	2012-05-24 10:57:06 -04:00
VariantContextBenchmark.java	Cleanup Genotypes	2012-06-14 16:42:36 -04:00
VariantContextTestProvider.java	Updates to VCF processing for better BCF processing	2012-07-08 15:44:33 -07:00
VariantContextUnitTest.java	Add unit tests for VariantContextBuilder.rmAttribute() and .attribute()	2012-06-25 12:05:04 -04:00
VariantContextUtilsUnitTest.java	Finalizing new Genotype object and associated routines	2012-06-14 16:42:25 -04:00
VariantJEXLContextUnitTest.java	Killing the final versions of old new VariantContext interface	2011-11-18 21:32:43 -05:00