aaron 3d3d19a6a7 the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date. ... a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc). Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3104 348d0f76-0448-11de-a6fe-93d51630548a		2010-03-31 22:39:56 +00:00
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alignment	oops - didn't mean to check this in	2010-03-02 20:28:22 +00:00
gatk	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
oneoffprojects/walkers/varianteval2	Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics	2010-03-29 13:32:00 +00:00
playground	Moving VariantsToVCF to core.	2010-03-26 18:55:12 +00:00
utils	Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP	2010-03-14 21:08:14 +00:00
BaseTest.java	added root GATKData variable	2010-02-12 15:25:34 +00:00
TrivialInstrumenter.java	fixed a bunch of comments and license headers.	2009-06-10 14:10:46 +00:00
WalkerTest.java	another test-with-multiple outputs fix	2010-03-04 22:46:15 +00:00