From 7a10c40fb39dbc47065cb7a6647b183c30afb23d Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 28 Jan 2010 21:16:21 +0000
Subject: [PATCH] Much clearer (and, like, not totally incorrect)
 implementation of isNovel

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2725 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/vcf/VCFRecord.java           | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
index 0aa5ae2bc..6afb03371 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFRecord.java
@@ -325,7 +325,16 @@ public class VCFRecord implements Variation, VariantBackedByGenotype {
     }
 
     public boolean isNovel() {
-        return ( mID != null || mInfoFields.get(HAPMAP2_KEY) != null || mInfoFields.get(HAPMAP3_KEY) != null || mInfoFields.get(DBSNP_KEY) != null);
+        return mID == null && ! isInHapmap();
+    }
+
+    public boolean isInHapmap() {
+        boolean inHapmap;
+        if ( mInfoFields.get(HAPMAP2_KEY) != null && mInfoFields.get(HAPMAP2_KEY).equals("1") ) {
+            return true;
+        } else {
+            return ( mInfoFields.get(HAPMAP3_KEY) != null && mInfoFields.get(HAPMAP3_KEY).equals("1") );
+        }
     }
 
     public char getAlternativeBaseForSNP() {