aaron 782e0018e4 removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come. ... *** Three integration tests had to change: *** RecalibarationWalkersIntegrationTest: One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates) SequenomValidationConverterIntegrationTest: relies on Plink ROD which we've removed. PileupWalkerIntegrationTest: we no longer have implicit interval tracks, so there isn't a rod name over the specified region. Otherwise the same result. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-15 22:54:49 +00:00
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bed	Moved stingexception	2010-09-12 14:39:22 +00:00
collections	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +00:00
genotype	removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.	2010-09-15 22:54:49 +00:00
interval	Missed update input	2010-09-12 15:46:13 +00:00
pileup	Replaced placeholder support for splitting by read group with read support (sorry everyone), and added relatively comprehensive unit tests to ensure that splitting by read group works.	2010-09-01 22:24:50 +00:00
sam	Rev the reservoir downsampler to support partitioning through a functor.	2010-04-21 19:50:26 +00:00
threading	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
BaseUtilsUnitTest.java	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
GenomeLocParserTestUtils.java	Added a back door so that integration tests can reset the sequence dictionary	2010-09-14 18:58:08 +00:00
GenomeLocParserUnitTest.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
GenomeLocSortedSetUnitTest.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
GenomeLocUnitTest.java	Removed hard-coded pointers to references	2010-08-04 17:59:37 +00:00
MathUtilsUnitTest.java	A utility class that computes running average and standard deviation for a stream of numbers it is being fed with. Updates mean/stddev on the fly and does not cache the observations, so it uses no memory and also should be stable against overflow/loss of precision. Simple unit test is also provided (does *not* stress-test the engine with millions of numbers though).	2010-08-04 21:39:02 +00:00
PathUtilsUnitTest.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
ReservoirDownsamplerUnitTest.java	Checking in downsampling iterator alongside LocusIteratorByState, and removing	2010-05-17 21:00:44 +00:00
UtilsUnitTest.java	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