Mark DePristo 773af05980 Intermediate commit for proper error handling in the NanoScheduler ... -- Refactored error handling from HMS into utils.TraversalErrorManager, which is now used by HMS and will be usable by NanoScheduler -- Generalized EngineFeaturesIntegrationTest to test map / reduce error throwing for nt 1, nt 2 and nct 2 (disabled) -- Added unit tests for failing input iterator in NanoScheduler (fails) -- Made ErrorThrowing NanoScheduable		2012-09-19 17:03:13 -04:00
..
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	Intermediate commit for proper error handling in the NanoScheduler	2012-09-19 17:03:13 -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	Intermediate commit for proper error handling in the NanoScheduler	2012-09-19 17:03:13 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Renaming -cnt to -nct for consistency	2012-09-05 21:13:19 -04:00