Mark DePristo 5894d045cb Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests ... -- This version of BCF should actually work properly for most files, assuming headers are properly defined. -- Lots of bug fixes to BCF2 codec -- Genotype getPhredScaledQual is now an int, returning -1 if there's no QUAL. NOTE THIS SEMANTICS change -- Equals() method for GenotypeLikelihoods, using PLs. -- VCFCodec now longer adds empty bindings to missing input field values. NOTE THIS CHANGE -- VCs can be marked as fully decoded, so that when fullyDecode() is called it returns itself, instead of doing the decoding work. The BCF2 codec now makes VCs marked as fully decoded -- stringToBytes returns empty list for null or "" string in BCF2Encoder -- Proper handling of genotype ordering in BCF2 reader / writer -- Removed the crazy slow noDups and sameSamples tests that were slowing down unit and integration tests totally unnecessarily -- Many failing MD5s now due to double -> int change in GQ, will update later		2012-05-27 11:17:17 -04:00
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writer	Bugfixes and testdata cleanup	2012-05-24 13:26:05 -04:00
AlleleUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenotypeLikelihoodsUnitTest.java	99% working version of BCF2 encoder / decoder	2012-05-24 10:57:05 -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	Don't try to share BCF2 yet	2012-05-24 10:57:06 -04:00
VariantContextBenchmark.java	Rev Tribble to r97, adding binary feature support	2012-05-03 07:31:48 -04:00
VariantContextTestProvider.java	Bugfixes and code cleanup throughout so BCF2 passes VC -> BCF -> VC tests	2012-05-27 11:17:17 -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