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gatk-3.8/public/java/test/org/broadinstitute/sting/utils/variantcontext
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Mark DePristo 64d4238e2f 99% working version of BCF2 encoder / decoder 
-- fixed final bugs with PL encoding / decoding
-- Ready for testing by other members of the group
-- Current performance numbers aren't so great, but they will improve in the next phase of BCF2 optimizations
-- Fixed a nasty bug in the filter field
-- Not that some (many?) GATK tools won't work with BCF because they internally assume values are Strings not their true types

Read 1500 genotypes file in VCF -> VCF : 11 seconds
Read 1500 genotypes file in VCF -> BCF : 9.5 seconds

VariantEval 1500 genotypes file in VCF : 3 seconds
VariantEval 1500 genotypes file in BCF : 3 seconds
 		2012-05-24 10:57:05 -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 99% working version of BCF2 encoder / decoder 2012-05-24 10:57:05 -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