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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo fee9b367e4 VariantContext genotypes are now stored as GenotypeMap objects 
-- Enables further sophisticated optimizations, as this class can be smarter about storing the data and will directly support operations like subset to samples
-- All instances in the gatk that used Map<String, Genotype> now use GenotypeMap type.
-- Amazingly, there were many places where HashMap<String, Genotype> is used, so that the order of the genotypes is technically undefined and could be dangerous.  Now everything uses GenotypeMap with a specific ordering of samples (by name)
-- Integrationtests updated and all pass
 		2011-11-11 15:00:35 -05:00
..
R No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
baq Putative fix for BAQ array out of bounds 2011-09-21 11:25:08 -04:00
clipreads GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
codecs Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative. 2011-10-27 23:55:11 -04:00
collections Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
fasta Reduced the number of combinations being tested here, which was overkill 2011-09-01 10:42:43 -04:00
fragments GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
genotype/vcf VariantContext genotypes are now stored as GenotypeMap objects 2011-11-11 15:00:35 -05:00
interval Added integration test for intervals from bed file 2011-11-09 15:34:19 -05:00
io Embedding gsalib source and queueJobReport R scripts in the dist and package jars. 2011-10-24 15:58:34 -04:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
report Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
runtime No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
sam Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
text GATKReport v0.2: 2011-08-03 00:24:47 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext VariantContext genotypes are now stored as GenotypeMap objects 2011-11-11 15:00:35 -05:00
BaseUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocParserUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocSortedSetUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MWUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ReadUtilsUnitTest.java Adding a synthetic read for filtered data 2011-11-09 20:16:22 -05:00
ReservoirDownsamplerUnitTest.java Moving reduced read functionality into GATKSAMRecord 2011-10-21 13:28:05 -04:00
SimpleTimerUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
UtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00