hanna 497bcbcbb7 Recent changes to the build system make the build system complain loudly about ... pieces of core that depend on playground. Most of these have been eliminated by (temporarily) promoting Aaron's report system to core in this checkin. I'll follow up with other changes in separately. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-24 22:09:12 +00:00
..
alignment	all fixed..thanks Matt!	2010-09-10 06:18:59 +00:00
commandline	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
datasources/pipeline	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00
gatk	GATK now detects and UserExceptions when human lexicographically sorted data is provided	2010-09-24 15:19:48 +00:00
oneoffprojects/walkers	The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder.	2010-09-21 18:21:22 +00:00
playground/gatk/walkers	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
utils	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
BaseTest.java	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
WalkerTest.java	Added a back door so that integration tests can reset the sequence dictionary	2010-09-14 18:58:08 +00:00