depristo 85553cf5cb V2 cleaner, easily testing, shared memory and distributed GATK job management. Serious unit testing. Very much cleaner processing. Some code cleanup remains in removing now unused classes but the system is ready for general testing. Confirmed that one can run the UG 100 ways parallel without error, but edge cases may remain. ... See documentation at: http://www.broadinstitute.org/gsa/wiki/index.php/Parallelism_and_the_GATK#Distributed_Parallelism_.28Experimental.29 for examples on how to run this, or the testing Scala script git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5032 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-20 12:58:13 +00:00
..
alignment	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
commandline	Fixed long-standing bug reported by Mauricio where @Arguments assigned to	2011-01-12 22:18:24 +00:00
datasources/pipeline	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
gatk	Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.	2011-01-20 12:54:03 +00:00
jna	Removed LibBat.SUB2_BSUB_BLOCK since the use of it exits the JVM.	2010-12-14 19:57:20 +00:00
oneoffprojects/walkers	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
playground/gatk/walkers	consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation).	2010-11-30 00:01:56 +00:00
utils	V2 cleaner, easily testing, shared memory and distributed GATK job management. Serious unit testing. Very much cleaner processing. Some code cleanup remains in removing now unused classes but the system is ready for general testing. Confirmed that one can run the UG 100 ways parallel without error, but edge cases may remain.	2011-01-20 12:58:13 +00:00
BaseTest.java	Updated the HG19 reference from v0 to v1 after the v0 was zeroed out.	2011-01-19 20:30:25 +00:00
StingTextReporter.java	Cleanup testng listener configuration.	2010-11-15 23:43:14 +00:00
WalkerTest.java	Remove testWalkerUnitTest; it doesn't actually do anything and just adds	2011-01-13 19:02:00 +00:00