hanna cba18116e4 A significant refactoring of the ROD system, done largely to simplify the process of ... streaming/piping VCFs into the GATK. Notable changes: - Public interface to RMDTrackBuilder is greatly simplified; users can use it only to build RMDTracks and lookup codecs. - RODDataSource and RMDTrack are no longer functionally at the same level; RODDataSources now manage RMDTracks on behalf of the GATK, and the only direct consumers of the RMDTrack class are the walkers that feel the need to access the ROD system directly. (We need to stamp out this access pattern. A few minor warts were introduced as part of this process, labeled with TODOs. These'll be fixed as part of the VCF streaming project. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4915 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-31 04:52:22 +00:00
..
helpers	We no longer require dbSNP files to be of the dbsnp rod-type; VCFs will do (provided they are bound to the name 'dbsnp')	2010-11-30 03:25:18 +00:00
FeatureToGATKFeatureIterator.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
FlashBackIterator.java	adding the initial ROD for Reads support; more convenience methods in ReadMetaDataTracker to come.	2010-03-03 15:56:44 +00:00
GATKFeature.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
GATKFeatureIterator.java	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
LocationAwareSeekableRODIterator.java	fixes for parallel processing problems with Tribble, a small bug in the resource pool, and some more documentation.	2010-05-12 06:13:26 +00:00
RMDIntervalGenerator.java	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
RMDTriplet.java	A significant refactoring of the ROD system, done largely to simplify the process of	2010-12-31 04:52:22 +00:00
RODRecordList.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
StringToGenomeLocIteratorAdapter.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00