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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo d37a8a0bc8 Efficient Genotype object Intermediate commit 
-- 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!
 		2012-06-14 16:42:24 -04:00
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alignment
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commandline Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
gatk Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
jna Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
utils Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
BaseTest.java Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
MD5DB.java Made GQ an int, not a float. Updated VC code and lots of corresponding MD5s 2012-05-28 20:20:05 -04:00
MD5Mismatch.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
StingTextReporter.java
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WalkerTest.java First step towards an efficient Genotype object 2012-06-14 16:42:23 -04:00