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
of a sequence dictionary and related info. This will hopefully eliminate the cases in
which the refseq track depends a sequence dictionary / contig parser that hasn't been
specified.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4700 348d0f76-0448-11de-a6fe-93d51630548a
*** Three integration tests had to change: ***
RecalibarationWalkersIntegrationTest:
One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates)
SequenomValidationConverterIntegrationTest:
relies on Plink ROD which we've removed.
PileupWalkerIntegrationTest:
we no longer have implicit interval tracks, so there isn't a rod name over the specified region. Otherwise the same result.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a
- changed to a better method for getting headers from Codecs
- some removal of old commented out code in the GATKAgrumentCollection
- changes for the rename of FeatureReader to FeatureSource
- removed the old Beagle ROD
- cleaned up some of the code in SampleUtils
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3826 348d0f76-0448-11de-a6fe-93d51630548a
hanna
aaron
depristo