From c203e0fb027570d2b2c686dc2ad7f735e302f87f Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 2 Aug 2010 12:24:11 +0000 Subject: [PATCH] Added JEXL support for hetCount, homRefCount, and homVarCount in VCs. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3914 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/contexts/variantcontext/VariantJEXLContext.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java index 5d953c06e..6aa74887b 100644 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java @@ -67,9 +67,9 @@ class VariantJEXLContext implements JexlContext { x.put("FILTER", new AttributeGetter() { public Object get(VariantContext vc) { return vc.isFiltered() ? "1" : "0"; }}); // x.put("GT", new AttributeGetter() { public Object get(VariantContext vc) { return g.getGenotypeString(); }}); -// x.put("isHomRef", new AttributeGetter() { public Object get(VariantContext vc) { return g.isHomRef() ? "1" : "0"; }}); -// x.put("isHet", new AttributeGetter() { public Object get(VariantContext vc) { return g.isHet() ? "1" : "0"; }}); -// x.put("isHomVar", new AttributeGetter() { public Object get(VariantContext vc) { return g.isHomVar() ? "1" : "0"; }}); + x.put("homRefCount", new AttributeGetter() { public Object get(VariantContext vc) { return vc.getHomRefCount(); }}); + x.put("hetCount", new AttributeGetter() { public Object get(VariantContext vc) { return vc.getHetCount(); }}); + x.put("homVarCount", new AttributeGetter() { public Object get(VariantContext vc) { return vc.getHomVarCount(); }}); } public VariantJEXLContext(VariantContext vc) {