hanna 83b8676b69 Hack to fix mysterious disappearing read attributes. Ultimately caused ... by the fact that the GATKSAMRecord, by design, needs to both inherit from SAMRecord and wrap a 'member' SAMRecord, and method calls that aren't implemented as explicit passthroughs can compromise the content of the SAMRecord in subtle ways. Will be automatically fixed when Picard moves to a lightweight SAMRecord interface rather than the current heavyweight implementation. But in the short-term, there's no obvious fix. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4489 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-13 19:06:54 +00:00
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arguments	Removing the obsolete --hapmap and --hapmap_chip options	2010-08-31 16:57:05 +00:00
contexts/variantcontext	A fix for an integration test that was broken by on-the-fly indexing. Also, better reporting of Tribble exceptions in GATK integration tests. Trying to get the tests back up and running...	2010-10-12 18:39:56 +00:00
datasources	Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are:	2010-09-28 02:16:25 +00:00
executive	A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests.	2010-04-08 06:14:15 +00:00
filters	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
iterators	Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.	2010-09-25 02:49:30 +00:00
refdata	High performance version of standard vcf writer. New general static Tribble class for common constants, including general .idx constant and functions to get standard index name for a given file.	2010-10-08 19:53:21 +00:00
traversals	Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.	2010-09-25 02:49:30 +00:00
walkers	Hack to fix mysterious disappearing read attributes. Ultimately caused	2010-10-13 19:06:54 +00:00
WalkerManagerUnitTest.java	Basic unit tests for WalkerManager.	2010-09-30 19:27:41 +00:00