From 195f0c3e983abbeb22ec1fbbcec4862ca789121e Mon Sep 17 00:00:00 2001
From: sathibault <thibault@gmvhdl.com>
Date: Fri, 17 May 2013 08:30:23 -0500
Subject: [PATCH] Disable CnyPairHMM

---
 .../sting/utils/pairhmm/CnyPairHMM.java               | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
index 51611bb08..a8f07a2ea 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java
@@ -18,7 +18,16 @@ public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
     private List<HmmInput> pending = new LinkedList<HmmInput>();
 
     static public boolean isAvailable() {
-	return true;
+	return false;
+    }
+
+    public void initialize( final int READ_MAX_LENGTH, final int HAPLOTYPE_MAX_LENGTH ) {
+	if (!loaded) {
+	    //	    System.loadLibrary("gmvhdl_gatk_hmm");
+	    //	    initFpga();
+	    loaded = true;
+	}
+	System.out.println("FPGA HMM Initialized");
     }
 
     public void batchAdd(final List<Haplotype> haplotypes,