hanna dc5f858d29 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4190 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-01 22:24:50 +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	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +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
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
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