d37a8a0bc8
-- Created a new Genotype interface with a more limited set of operations -- Old genotype object is now SlowGenotype. New genotype object is FastGenotype. They can be used interchangable -- There's no way to create Genotypes directly any longer. You have to use GenotypeBuilder just like VariantContextBuilder -- Modified lots and lots of code to use GenotypeBuilder -- Added a temporary hidden argument to engine to use FastGenotype by default. Current default is SlowGenotype -- Lots of bug fixes to BCF2 codec and encoder. -- Feature additions -- Now properly handles BCF2 -> BCF2 without decoding or encoding from scratch the BCF2 genotype bytes -- Cleaned up semantics of subContextFromSamples. There's one function that either rederives or not the alleles from the subsetted genotypes -- MASSIVE BUGFIX in SelectVariants. The code has been decoding genotypes always, even if you were not subsetting down samples. Fixed! |
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| .. | ||
| datasources | ||
| downsampling | ||
| executive | ||
| filters | ||
| iterators | ||
| refdata | ||
| report | ||
| samples | ||
| traversals | ||
| walkers | ||
| EngineFeaturesIntegrationTest.java | ||
| GenomeAnalysisEngineUnitTest.java | ||
| WalkerManagerUnitTest.java | ||