From d07f3bb6f6728390294945c428be309ae6265e7d Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Nov 2009 04:20:35 +0000
Subject: [PATCH] Added methods to get strand bias and to test if record has
 allele freq or bias fields set.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1993 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/refdata/RodVCF.java            | 21 +++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
index 6026a83f0..98271b00b 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
@@ -78,6 +78,11 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         if (!this.isBiallelic()) throw new StingException("We're not bi-allelic.");
     }
 
+    public boolean hasNonRefAlleleFrequency() {
+        return (this.mCurrentRecord.getInfoValues().containsKey("AF") ||
+                (this.mCurrentRecord.getInfoValues().containsKey("AC") && this.mCurrentRecord.getInfoValues().containsKey("AN")));
+    }
+
     /**
      * get the frequency of this variant
      *
@@ -101,6 +106,22 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
         return 0.0;
     }
 
+    public boolean hasStrandBias() {
+        return this.mCurrentRecord.getInfoValues().containsKey("SB");
+    }
+
+    /**
+     * get the strand bias of this variant
+     *
+     * @return StrandBias with the stored slod
+     */
+    public double getStrandBias() {
+        assertNotNull();
+        if (this.mCurrentRecord.getInfoValues().containsKey("SB"))
+            return Double.valueOf(this.mCurrentRecord.getInfoValues().get("SB"));
+        return 0.0;
+    }
+
     /** @return the VARIANT_TYPE of the current variant */
     @Override
     public VARIANT_TYPE getType() {