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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo c8ed0bfc4c Edge case fixes for BCF2 
--handle entirely missing GT in a sample in decodeGenotypeAlleles
--Create MAX_ALLELES_IN_GENOTYPES constant in BCF2Utils, and extracted its use inline from the code
-- Generalized genotype writing code to handle ploidy != 2 and variable ploidy among samples
-- Remove special case inline treatment of case where all samples have no GT field values, and moved this into calcVCFGenotypeKeys
-- Removed restriction on getPloidy requiring ploidy > 1.  It's logically find to return 0 for a no called sample
-- getMaxPloidy() in VC that does what it says
-- Support for padding / depadding of generic genotype fields
 		2012-05-24 10:57:06 -04:00
..
writer Near final BCF2 implementation 2012-05-24 10:57:02 -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 99% working version of BCF2 encoder / decoder 2012-05-24 10:57:05 -04:00
VariantContextBenchmark.java Rev Tribble to r97, adding binary feature support 2012-05-03 07:31:48 -04:00
VariantContextTestProvider.java Edge case fixes for BCF2 2012-05-24 10:57:06 -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