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gatk-3.8/java/test/org/broadinstitute/sting/utils
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hanna cb144734c0 Getting rid of GenotypeWriter interface. Of note: 
- GATKVCFWriter deleted, to be replaced if absolutely necessary when VCF writing goes into Tribble.
- VCFWriter is now an interface, for easier redirection.
- VCFWriterImpl fleshes out the VCFWriter interface.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4026 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-13 16:33:22 +00:00
..
bed Removed hard-coded pointers to references 2010-08-04 17:59:37 +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 Getting rid of GenotypeWriter interface. Of note: 2010-08-13 16:33:22 +00:00
interval providing a way to specify how you'd like -BTI combined with your -L options; set BTIMR to either UNION (default) or INTERSECTION. 2010-08-09 14:00:52 +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
GenomeLocParserUnitTest.java Refactoring intervals, separating the process of parsing interval lists, 2010-04-13 15:50:38 +00:00
GenomeLocSortedSetUnitTest.java add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal. 2010-04-15 16:31:43 +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 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
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