gatk-3.8/public/java/test/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
..
commandline Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" 2012-09-10 15:52:39 -04:00
gatk Cleanup Exact model, better unit tests 2012-10-03 19:55:11 -07:00
jna Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
utils Commit changes in Variants To Binary Ped to the stable repository to be available prior to next release. 2012-09-27 00:13:32 -04:00
BaseTest.java Extensive unit tests, contacts, and documentation for RecalDatum 2012-07-31 08:11:03 -04:00
MD5DB.java Finalizing BCF2 mark III commit 2012-06-21 15:16:27 -04:00
MD5Mismatch.java Final updates to integration tests for BCF2 2012-05-24 10:58:59 -04:00
StingTextReporter.java
WalkerTest.java Renaming -cnt to -nct for consistency 2012-09-05 21:13:19 -04:00