aaron 3093a20a55 fixing VCF header format and info fields so that they propery emit the unbounded count value correctly for vcf4 or vcf3. Eric we should update the vcf4 spec page to indicate format fields are allowed to use the unbounded count as well (if this is true). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3707 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-01 22:02:16 +00:00
..
bed	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +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	fixing VCF header format and info fields so that they propery emit the unbounded count value correctly for vcf4 or vcf3. Eric we should update the vcf4 spec page to indicate format fields are allowed to use the unbounded count as well (if this is true).	2010-07-01 22:02:16 +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	IndexedFastaSequenceFile is now in Picard; transitioning to that implementation.	2010-07-01 04:40:31 +00:00
MathUtilsUnitTest.java	The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had	2010-04-20 15:26:32 +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