ebanks 47440bc029 - Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads. ... - Reimplemented optimization in UG to not call when there are no non-ref bases. - Compute reference confidence accurately in UG for ref calls. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2693 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-26 21:56:33 +00:00
..
arguments	Looks bigger than it is:	2010-01-15 00:14:35 +00:00
datasources	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	ant clean is your friend....fixed test code dependent on an interface change.	2010-01-22 20:07:46 +00:00
refdata	Refactoring and migration of new allele/variantcontext/genotype code into oneoffprojects. NOT FOR USE. PlinkRod commented out due to dependence on this new, rapidly changing interface.	2010-01-26 13:53:29 +00:00
traversals	First successful test of new sharding system prototype. Can traverse over reads from a single	2010-01-15 03:35:55 +00:00
walkers	- Removed max_coverage argument from UG; Aaron will set it up so that we don't call when the GATK had to drop reads.	2010-01-26 21:56:33 +00:00