From 551ce9130fa7d19b955c0cedca905557ceb44a55 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sat, 4 Apr 2009 21:31:16 +0000
Subject: [PATCH] added isBiallelic() to the AllelicVariant interface and to
 rodDbSNP implementation. We probably don't really know how to deal with
 non-biallelic sites just as yet...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@294 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/refdata/AllelicVariant.java | 8 ++++++++
 .../org/broadinstitute/sting/gatk/refdata/rodDbSNP.java   | 6 ++++++
 2 files changed, 14 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
index 720f5bc09..99160d2e0 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/AllelicVariant.java
@@ -119,4 +119,12 @@ public interface AllelicVariant extends Comparable<ReferenceOrderedDatum> {
      * @return
      */
     int getPloidy() throws IllegalStateException;
+    
+    /** Returns true if the site has at most two known or observed alleles (ref and non-ref), or false if there are > 2 allelic variants known or observed. When
+     * the implementing class is a genotype, alleles should be always counted including the reference allele whether it was observed in the particular
+     * individual or not: i.e. if the reference is 'C', then both 'CA' and 'AA' genotypes must be reported as bi-allelic, while 'AT' is <i>not</i> bi-allelic (since there are
+     * two allelic variants, 'A' and 'T' <i>in addition</i> to the (known) reference variant 'C'). 
+     * @return
+     */
+    boolean isBiallelic() ;
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
index 286b02b31..d62c9d067 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
@@ -222,4 +222,10 @@ public class rodDbSNP extends ReferenceOrderedDatum implements AllelicVariant {
 		// TODO Auto-generated method stub
 		return false;
 	}
+
+	@Override
+	public boolean isBiallelic() {
+		// TODO Auto-generated method stub
+		return observed.indexOf('/')==observed.lastIndexOf('/');
+	}
 }