Mark DePristo 24864fd5b0 GATK now writes BCF output to any file with .bcf extension ... -- Moved VCF and BCF writers to variantcontext.writers -- Updated vcf.jar build path -- Refactored VCFWriter and other code. Now the best (and soon to be only) way to create these files is through a factory method called VariantContextWriterFactory. Renamed the general VCFWriter interface to VariantContextWriter which is implemented by VCFWriter and BCF2Writer.		2012-05-24 10:57:00 -04:00
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AlleleUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenotypeLikelihoodsUnitTest.java	Fixing unit tests to register the user exception being thrown (instead of the NumberFormatException)	2012-04-23 10:06:51 -04:00
GenotypeUnitTest.java	Change interface to getNegLog10PError to getLog10PError	2011-11-18 21:07:30 -05:00
GenotypesContextUnitTest.java	GenotypesContext now updates cached data for add, set, replace operations when possible	2011-11-22 08:40:48 -05:00
VCFJarClassLoadingUnitTest.java	GATK now writes BCF output to any file with .bcf extension	2012-05-24 10:57:00 -04:00
VariantContextBenchmark.java	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
VariantContextUnitTest.java	New annotation for indels that describe if they're STR's and their characteristics. If an indel is a STR, 3 fields are added to INFO: STR (boolean), RU = repeat unit (String), RPA = number of repetitions per allele. So, for example, if ATATAT* context gets changed to ATAT and ATATATAT, then RU=AT and RPA=3,2,4. Will be made standard annotation shortly. Added unit tests for new functionality. Pending: refactor VariantContextUtils.isRepeat() to unify code, and fix VariantEval functionality.	2012-05-17 15:28:19 -04:00
VariantContextUtilsUnitTest.java	Modified UnitTests to respect reference padding	2012-04-06 16:27:20 -04:00
VariantJEXLContextUnitTest.java	Killing the final versions of old new VariantContext interface	2011-11-18 21:32:43 -05:00