From 7a04872a3f45d23efd1e91e41b08b7f30def8b3d Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Mon, 4 Jul 2011 20:33:59 -0400
Subject: [PATCH] bug fixes

---
 .../sting/gatk/walkers/variantutils/SelectVariants.java       | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 95e5ed934..e7331d646 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -246,8 +246,10 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                 afBoosts = new ArrayList<Double>();
                 logger.info("Reading in AF boost table...");
                 for ( final String line : new XReadLines( AF_FILE ) ) {
-                    System.out.println(line);
+                    //System.out.println(line);
                     final String[] vals = line.split("\t");
+                    if (vals[0].matches("midpoints"))
+                        continue;
                     double bkp = Double.valueOf(vals[0]);
                     double afb = Double.valueOf(vals[1]);
                     afBreakpoints.add(bkp);