From 50c32ce52e85a05fe252058e8ec72495b79adfe6 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Wed, 29 Jun 2011 21:39:53 -0400
Subject: [PATCH] VariantsToTableFix

---
 .../sting/gatk/walkers/variantutils/VariantsToTable.java     | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index 079fc7aba..2111b0959 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -173,7 +173,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
             if (field.equals("AF")) {
                      String afo = val;
 
-                     double af;
+                     double af=0;
                      if (afo.contains(",")) {
                          String[] afs = afo.split(",");
                          afs[0] = afs[0].substring(1,afs[0].length());
@@ -189,7 +189,8 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
 
                      }
                      else
-                         af = Double.valueOf(afo);
+                         if (!afo.equals("NA"))
+                             af = Double.valueOf(afo);
 
                 val = Double.toString(af);