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
..
AllLocusViewTest.java	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
CoveredLocusViewTest.java	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
LocusReferenceViewTest.java	Test updated. Now we do not throw an exception when locus interval is out of bounds, we just return silently a reference context trimmed to the current shard boundaries. New test checks for trimming.	2010-03-22 17:37:52 +00:00
LocusViewTemplate.java	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
ReadBasedReferenceOrderedViewTest.java	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
ReadReferenceViewTest.java	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
ReferenceOrderedViewTest.java	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
ReferenceViewTemplate.java	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00
ShardDataProviderTest.java	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00