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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo 1f45551a15 Bugfixes to G count types in VCF header 
-- Previously VCF header lines of count type G assumed that the sample would be diploid.
-- Generalized the code to take a VariantContext and return the right result for G count types by calling into the correct numGenotypes in GenotypeLikelihoods class
-- renamed calcNumGenotypes to numGenotypes, which uses a static cache in the class
-- calcNumGenotypes is private, and is used to build the static cache or to compute on the fly for uncached No. allele / ploidy combinations
-- VariantContext calls into getMaxPloidy in GenotypesContext, which caches the max ploidy among samples
-- Added extensive unit tests that compare A and G type values in genotypes
 		2012-06-26 15:28:34 -04:00
..
R AggregateMetrics: 2012-04-17 11:45:32 -04:00
activeregion Fixing ActivityProfile unit test. 2012-04-10 15:28:27 -04:00
baq Putative fix for BAQ array out of bounds 2011-09-21 11:25:08 -04:00
clipping Refactor on how RR treats soft clips 2012-06-21 14:02:03 -04:00
codecs Horrible bugfix to decodeLoc() in BCF2Codec 2012-06-26 15:28:32 -04:00
collections Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
crypt Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
fasta A few misc. residual errors in last commit 2012-06-21 16:04:25 -04:00
fragments GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
interval Cleanup of VCF header lines and constants, BCF2 bugfixes 2012-06-21 15:16:31 -04:00
io Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
recalibration The next round of BQSR optimizations: no more Long[] array creation 2012-06-14 00:05:42 -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 Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped 2012-04-27 09:58:38 -04:00
text AggregateMetrics: 2012-04-17 11:45:32 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext Bugfixes to G count types in VCF header 2012-06-26 15:28:34 -04:00
BaseUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
BitSetUtilsUnitTest.java Oops, forgot to push the unit tests 2012-06-12 11:38:30 -04:00
GenomeLocParserUnitTest.java During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice. 2011-11-17 13:56:42 -05:00
GenomeLocSortedSetUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java Support for list of known CNVs in VariantEval 2011-11-30 17:05:16 -05:00
HaplotypeUnitTest.java Adding genotype given alleles mode to the HaplotypeCaller. 2012-05-30 15:07:01 -04:00
MWUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtilsUnitTest.java minor misc optimizations to PairHMM 2012-04-18 15:02:26 -04:00
MedianUnitTest.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
PairHMMUnitTest.java Resolve merge conflicts 2012-04-18 16:25:03 -04:00
PathUtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
QualityUtilsUnitTest.java Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests. 2012-03-21 08:45:42 -04:00
ReservoirDownsamplerUnitTest.java Moving reduced read functionality into GATKSAMRecord 2011-10-21 13:28:05 -04:00
SimpleTimerUnitTest.java The right fix for this test is just to delete it. 2011-11-15 14:53:27 -05:00
UtilsUnitTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00