From c67ced5f3bb4dc12463022d72344ef541d03f7d9 Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Wed, 12 Mar 2014 09:55:35 -0400
Subject: [PATCH] Emit a warning whenever the VectorLoglessPairHMM is used

---
 .../sting/utils/pairhmm/VectorLoglessPairHMM.java             | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
index b94e7e3ec..e69d9ea50 100644
--- a/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
+++ b/protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java
@@ -117,6 +117,10 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
     //The constructor is called only once inside PairHMMLikelihoodCalculationEngine
     public VectorLoglessPairHMM() {
         super();
+
+        logger.warn("WARNING: the VectorLoglessPairHMM is an experimental implementation still under active development. " +
+                    "Use at your own risk!");
+
         synchronized(isVectorLoglessPairHMMLibraryLoaded) {
             //Load the library and initialize the FieldIDs
             if(!isVectorLoglessPairHMMLibraryLoaded) {