rpoplin 5ddc0e464a Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5536 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-29 21:04:09 +00:00
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HLAcaller	Committing the fragment-based calling code. Results look great in all datasets (will show this at 1000G this week with Ryan). Note that this is an intermediate commit. The code needs to be cleaned up and the fragmentation code needs to be moved up into LocusIteratorByState. This should all happen later this week, but I don't want Ryan to have to keep running from my own personal Sting directory. The current crappy implementation adds ~10% to the runtime, but that should all go away in the next iteration.	2011-01-23 05:04:17 +00:00
duplicates	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
validation	consolidating the checking of the RMD sequence dictionary against the reference into a single function, and adding an integration test to test that empty VCFs pass (both the indexing and the seq dictionary validation).	2010-11-30 00:01:56 +00:00
variantrecalibration	Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately.	2011-03-29 21:04:09 +00:00