gatk-3.8/public/java/test/org/broadinstitute/sting
Mark DePristo a3d896d80e Part I of creating a fast state space lookup for VE
-- Created a unit tested tree mapping from a List<String> -> integer (StratificationStates).  This class is the key infrastructure necessary to create a complete static mapping from all stratification combinations to an offset in a vector of EvalutionContexts for update in map.
-- Minor code cleanup throughout VE (removing unused headers, for example)
2012-03-30 15:31:53 -04:00
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
gatk Part I of creating a fast state space lookup for VE 2012-03-30 15:31:53 -04:00
jna When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter. 2011-12-16 18:09:25 -05:00
utils Forgot to add tolerance to new MathUtils unit tests 2012-03-28 08:18:36 -04:00
BaseTest.java CalibrateGenotypeLikelihoods now emits the position of the variant for debugging 2012-03-09 16:00:07 -05:00
MD5DB.java Merged bug fix from Stable into Unstable 2011-10-13 18:02:06 -04:00
MedianUnitTest.java Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably. 2012-03-05 08:28:42 -05:00
StingTextReporter.java
WalkerTest.java Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on. 2012-03-18 00:53:29 -04:00