gatk-3.8

Author	SHA1	Message	Date
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

Author

SHA1

Message

Date

bthomas

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

3 Commits (f34b4c6b82cf8ee68d08d0172ecb4970af8bf30f)