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6 Commits (1d68b28bbd2834f87ba81c79fe348451ab15d5e9)

Author SHA1 Message Date
hanna 3039c0de3c Retire old ROD syntax. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4564 348d0f76-0448-11de-a6fe-93d51630548a
 2010-10-22 23:52:11 +00:00
hanna 1fb8c86f6d Looks like we've got two competing models for an empty interval list: null and 
the empty list.  Score another victory for the integration tests.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4391 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 17:11:47 +00:00
hanna 78343be52c At some time in the recent past, we lost our ability to process the '-L all' 
argument.  Brought it back, and added an integrationtest to make sure it
stays around.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4390 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-30 15:58:43 +00:00
bthomas 96cccafb0d Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 
-- getToolkit().subContextFromSampleProperty(): filters a VariantContext to genotypes that come from samples that have a given property value
-- getToolkit().getSamplesWithProperty(): gets all samples with a given property
-- getToolkit().getSamplesFromVariantContext(): sample objects that are referenced by name in a VariantContext



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4361 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-28 02:16:25 +00:00
kshakir edaa278edd Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 
This will allow other programs like Queue to reuse the functionality.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-25 02:49:30 +00:00
kshakir 4ed9f437e9 Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 
The GAE half has all the walker specific code.  The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
 2010-09-23 23:28:55 +00:00