aaron 611d834092 a couple of VCF 4 improvements: ... -Validation of INFO and FORMAT fields. -Conversion to the the correct type for info fields (i.e. allele frequency is now stored as a float instead of a string). -Checks for CNV style alternate allele encodings( i.e. <INS:ME:L1>), right now we exception out. Maybe we should just warn the user? -Tests for the multiple-base polymorphism allele case. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3622 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-23 20:21:43 +00:00
..
features/vcf4	a couple of VCF 4 improvements:	2010-06-23 20:21:43 +00:00
tracks	updating the tribble library to include the reference dictionary reading / writing. We now check the dictionaries of any tracks that have them against the reference (all new tribble tracks and out-of-date tracks will have this). Also renamed some classes to be more reflective of their function.	2010-06-04 06:34:26 +00:00
utils	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
PlinkRodUnitTest.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
ReadMetaDataTrackerUnitTest.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
ReferenceOrderedDataUnitTest.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
RodGLFUnitTest.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
TabularRODUnitTest.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
VariantContextAdaptorsUnitTest.java	Restructuring of ReferenceContext and ReadWalkers to accept a ReferenceContext. Now ReferenceContext is byte[] backed not char[]. Please no more chars for the reference. All of the tests pass now. Coming check-ins are going to clean up the char / byte problems in the GATK	2010-05-19 23:27:55 +00:00