kshakir 8855f080c2 For the fullCallingPipeline.q: ... - Reading the refseq table from the YAML if not specified on the command line. - Removed obsolete -bigMemQueue now that CombineVariants runs in 4g. - Added a -mountDir /broad/software option to work around adpr automount issues. - Merged the LSF preexec used for automount into the shell script used to execute tasks. - Using the LSF C Library to determine when jobs are complete instead of postexec. - Updated queue.sh to match the changes above. - Updated the FCPTest to match the changes above. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5036 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-20 22:34:43 +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	Some refactoring and cleanup around the area of my sleep-deprived integration	2011-01-20 15:03:14 +00:00
jna	For the fullCallingPipeline.q:	2011-01-20 22:34:43 +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