From 0226412b11a9bb1a9085d0f365e65219d3b26cb2 Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 14 Jul 2010 19:01:11 +0000 Subject: [PATCH] Add GQ to list of genotype attributes for reg exp git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3791 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/contexts/variantcontext/VariantJEXLContext.java | 6 ++++-- 1 file changed, 4 insertions(+), 2 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 be41155fd..ece9d8481 100644 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java @@ -28,6 +28,7 @@ import org.apache.commons.jexl2.MapContext; //import org.apache.commons.jexl2.JexlHelper; import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.Utils; +import org.broad.tribble.vcf.VCFConstants; import java.util.*; @@ -167,7 +168,7 @@ class JEXLMap implements Map { infoMap.put("CHROM", vc.getLocation().getContig()); infoMap.put("POS", String.valueOf(vc.getLocation().getStart())); infoMap.put("TYPE", vc.getType().toString()); - infoMap.put("QUAL", String.valueOf(10 * vc.getNegLog10PError())); + infoMap.put("QUAL", String.valueOf(vc.getPhredScaledQual())); // add alleles infoMap.put("ALLELES", Utils.join(";", vc.getAlleles())); @@ -193,10 +194,11 @@ class JEXLMap implements Map { // add specific genotype if one is provided if ( g != null ) { - infoMap.put("GT", g.getGenotypeString()); + infoMap.put(VCFConstants.GENOTYPE_KEY, g.getGenotypeString()); infoMap.put("isHomRef", g.isHomRef() ? "1" : "0"); infoMap.put("isHet", g.isHet() ? "1" : "0"); infoMap.put("isHomVar", g.isHomVar() ? "1" : "0"); + infoMap.put(VCFConstants.GENOTYPE_QUALITY_KEY, String.valueOf(g.getPhredScaledQual())); for ( Map.Entry e : g.getAttributes().entrySet() ) infoMap.put(e.getKey(), String.valueOf(e.getValue())); }