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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo dfee17a672 Generalize / unify code for handling strings 
-- List<String> is converted inside of the codec to a collapsed string, and exploded in the decoder.
-- Unified the type conversion code in BCFWriter to simply the mapping from VCF type => BCF type and special value recoding
-- Code cleanup and renaming
 		2012-05-24 10:57:02 -04:00
..
writer Testing of BCF codec 2012-05-24 10:57:01 -04:00
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
VariantContextTestProvider.java Generalize / unify code for handling strings 2012-05-24 10:57:02 -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