From b7e9c342c7aa92098efd83594960c17f38d34b2a Mon Sep 17 00:00:00 2001
From: Ryan Poplin <rpoplin@broadinstitute.org>
Date: Sun, 17 Feb 2013 11:09:00 -0500
Subject: [PATCH] Reducing the size of the reference padding in the
 HaplotypeCaller.

---
 .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index a8996c980..1dfec494a 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -270,7 +270,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
     private CachingIndexedFastaSequenceFile referenceReader;
 
     // reference base padding size
-    private static final int REFERENCE_PADDING = 900;
+    private static final int REFERENCE_PADDING = 400;
 
     // bases with quality less than or equal to this value are trimmed off the tails of the reads
     private static final byte MIN_TAIL_QUALITY = 20;