From 7ffcade3c3bd2d28e875dc443a22e061104d1612 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 17 Feb 2011 22:37:38 +0000
Subject: [PATCH] Added MNP to recognized and counted event types

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5266 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/varianteval/evaluators/CountVariants.java | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index 6340ab813..d99dc7ac7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -33,6 +33,8 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
 
     @DataPoint(description = "Number of snp loci")
     public long nSNPs = 0;
+    @DataPoint(description = "Number of mnp loci")
+    public long nMNPs = 0;
     @DataPoint(description = "Number of insertions")
     public long nInsertions = 0;
     @DataPoint(description = "Number of deletions")
@@ -40,6 +42,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
     @DataPoint(description = "Number of complex loci")
     public long nComplex = 0;
 
+
     @DataPoint(description = "Number of no calls loci")
     public long nNoCalls = 0;
     @DataPoint(description = "Number of het loci")
@@ -97,6 +100,10 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                 nSNPs++;
                 if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
                 break;
+            case MNP:
+                nMNPs++;
+                if (vc1.getAttributeAsBoolean("ISSINGLETON")) nSingletons++;
+                break;
             case INDEL:
                 if (vc1.isInsertion()) nInsertions++;
                 else nDeletions++;