chartl 7c9ef59d65 This is simultaneously a minor and major change to VariantEval, so take heed: ... The core walker has been modified so that when variant contexts (eval and comp) are subset to command-line-specified sample(s), the chromosome count annotations (AC/AN/AF) are altered to reflect the AC/AN/AF of only those samples involved in the comparison. No more getting AC500 when you're comparing a 10-sample overlap. Interestingly enough, this didn't break any integration tests. GenotypeConcordance now has two additional tables: Allele Count Statistics, and Allele Count Summary Statistics. These work exactly identically to the Sample Statistics and Sample Summary Statistics tables, except that the partition being used is no longer the sample, but instead the allele count of the variant sites. These tables stratify by both eval and comp ACs, e.g. evalAC0 evalAC1 evalAC2 compAC0 compAC1 compAC2 Differences with previous integration tests were verified to only be in the Allele Count tables (by grepping them out of the diff); a new test has been added for the simple case of an AC=1 site in the eval becoming an AC=2 site in the comp. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4491 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-13 22:26:15 +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	This is simultaneously a minor and major change to VariantEval, so take heed:	2010-10-13 22:26:15 +00:00
WalkerManagerUnitTest.java	Basic unit tests for WalkerManager.	2010-09-30 19:27:41 +00:00