hanna c2e8c460cb Factor out all testing dependencies into a separate test configuration and ... only download that test configuration when running unit/integration tests. This means that the build will (hopefully) never break because it can't fetch a file that isn't required for the GATK to run. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5775 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-05 22:42:11 +00:00
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providers	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
reads	Factor out all testing dependencies into a separate test configuration and	2011-05-05 22:42:11 +00:00
rmd	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
sample	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