fromer a7af1a164b Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4577 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-27 01:50:36 +00:00
..
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	Updated MNP merging to merge VC records if any sample has a haplotype of ALT-ALT, since this could possibly change annotations. Note that, besides the "interesting" case of an ALT-ALT MNP in a pair of HET sites, this could even occur if two records are hom-var (irrespective of using phasing). Note also that this procedure may generate more than one ALT allele.	2010-10-27 01:50:36 +00:00
WalkerManagerUnitTest.java	Basic unit tests for WalkerManager.	2010-09-30 19:27:41 +00:00