From 74087c44ae9b240997777b78511add983dd86aa9 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 4 Oct 2010 12:37:36 +0000
Subject: [PATCH] Fixed a bug which caused a parsing exception when there was a
 variant with a dp field of ".", e.g. "GT:DP  0/1:." -- which can happen when
 using imputation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4420 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/SelectVariants.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 9de8769f3..a15173725 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -255,7 +255,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                 else if (g.isHomVar()) { alleleCount += 2; }
                 
                 String dp = (String) g.getAttribute("DP");
-                if (dp != null) {
+                if (dp != null && ! dp.equals(".")) {
                     depth += Integer.valueOf(dp);
                 }
             }