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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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ebanks 341e752c6c 1) AlleleBalance is no longer a standard annotation, but the Allelic Depth (AD) is for each sample. 
2) Small fixes in the VCFWriter:
a) Trailing missing values weren't being removed if their count was > 1 (e.g. ".,.")
b) We were handling key values that were Lists, but not Arrays.  We now handle both.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3956 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-06 12:05:14 +00:00
..
arguments Experimental versions of downsampler and Ryan's deduper are now available either 2010-05-19 05:40:05 +00:00
contexts/variantcontext 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
datasources Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
executive 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
filters 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
io 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
iterators Removed hard-coded pointers to references 2010-08-04 17:59:37 +00:00
refdata 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
traversals IndexedFastaSequenceFile is now in Picard; transitioning to that implementation. 2010-07-01 04:40:31 +00:00
walkers 1) AlleleBalance is no longer a standard annotation, but the Allelic Depth (AD) is for each sample. 2010-08-06 12:05:14 +00:00