rpoplin af84462f3e The dev team has decided to change the filter that is added to records that are set to monomorphic by Beagle. It no longer lists the reference allele. Added those filters to the header of the output VCF file. Finally, we no longer use R2=NaN values coming from Beagle. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4757 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-30 17:19:54 +00:00
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arguments	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
contexts/variantcontext	JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts	2010-11-17 16:08:16 +00:00
datasources	Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.	2010-11-19 19:59:05 +00:00
executive	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
filters	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
iterators	Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.	2010-11-19 19:59:05 +00:00
refdata	Change the interface for RMDTrackBuilder, therefore always mandating the specification	2010-11-17 19:00:17 +00:00
traversals	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
walkers	The dev team has decided to change the filter that is added to records that are set to monomorphic by Beagle. It no longer lists the reference allele. Added those filters to the header of the output VCF file. Finally, we no longer use R2=NaN values coming from Beagle.	2010-11-30 17:19:54 +00:00
WalkerManagerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00