aaron 72ae81c6de VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include: ... - Tribble is included directly in the GATK repo; those who have access to commit to Tribble can now directly commit from the GATK directory from Intellij; command line users can commit from inside the tribble directory. - Hapmap ROD now in Tribble; all mentions have been switched over. - VariantContext does not know about GenomeLoc; use VariantContextUtils.getLocation(VariantContext vc) to get a genome loc. - VariantContext.getSNPSubstitutionType is now in VariantContextUtils. - This does not include the checked-in project files for Intellij; still running into issues with changes to the iml files being marked as changes by SVN I'll send out an email to GSAMembers with some more details. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3954 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-05 18:47:53 +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	VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:	2010-08-05 18:47:53 +00:00
interval	A simple utility class that implements a merging Iterator<GenomeLoc> built over an interval or bed file (this is NOT a rod, but rather a direct line-by-line file reader that converts strings to genome locs on the fly and merges overlapping intervals)	2010-06-14 15:54:37 +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