gatk-3.8

Commit Graph

Author	SHA1	Message	Date
ebanks	961ca05abc	Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a	2010-04-11 01:43:07 +00:00
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
ebanks	73a14a985b	Moving VariantsToVCF to core. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a	2010-03-26 18:55:12 +00:00

Author

SHA1

Message

Date

ebanks

961ca05abc

Removed outdated Sequenom rod and renamed HapMapGenotypeROD to HapMapROD.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3149 348d0f76-0448-11de-a6fe-93d51630548a

2010-04-11 01:43:07 +00:00

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

ebanks

73a14a985b

Moving VariantsToVCF to core.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3078 348d0f76-0448-11de-a6fe-93d51630548a

2010-03-26 18:55:12 +00:00

3 Commits (961ca05abc64cbb5dc6129b5a82dc53594d83378)