From a97576384d7953109de2a02c71b49e978f075738 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 25 Mar 2013 18:29:16 -0400
Subject: [PATCH] Fix bug in the HC not respecting the requested pruning

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

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 5849b5a0e..7e2211502 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
@@ -406,6 +406,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         // setup the assembler
         assemblyEngine = new DeBruijnAssembler( DEBUG, debugGraphTransformations, minKmer);
         assemblyEngine.setErrorCorrectKmers(errorCorrectKmers);
+        assemblyEngine.setPruneFactor(MIN_PRUNE_FACTOR);
         if ( graphWriter != null ) assemblyEngine.setGraphWriter(graphWriter);
         if ( useLowQualityBasesForAssembly ) assemblyEngine.setMinBaseQualityToUseInAssembly((byte)1);