gatk-3.8/public/java/src/org/broadinstitute/sting
Mark DePristo de941ddbbe Cleanup Exact model, better unit tests
-- Added combinatorial unit tests for both Diploid and General (in diploid-case) for 2 and 3 alleles in all combinations of sample types (i.e., AA, AB, BB and equiv. for tri-allelic).  More assert statements to ensure quality of the result.
-- Added docs (DOCUMENT YOUR CODE!) to AlleleFrequencyCalculationResult, with proper input error handling and contracts.  Made mutation functions all protected
-- No longer need to call reset on your AlleleFrequencyCalculationResult -- it'd done for you in the calculation function.  reset is a protected method now, so it's all cleaner and nicer this way
-- TODO still -- need to add edge-case tests for non-informative samples (0,0,0), for the impact of priors, and I need to add some way to test the result of the pNonRef
2012-10-03 19:55:11 -07:00
..
alignment Part II of GSA-462: Consistent RODBinding access across Ref and Read trackers 2012-08-30 10:15:10 -04:00
commandline Cleanup RefMetaDataTracker before refactoring ReadMetaDataTracker 2012-08-30 10:13:06 -04:00
gatk Cleanup Exact model, better unit tests 2012-10-03 19:55:11 -07:00
jna Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc. 2012-01-23 16:17:04 -05:00
queue Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release. 2012-07-23 16:32:31 -04:00
utils BQSR: allow logging recal table updates to a file 2012-10-01 14:18:34 -04:00