Merge pull request #626 from broadinstitute/intel_pairhmm

Removed scary warning messages for VectorPairHMM

protected/gatk-protected/src/main/java/org/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM.java

@@ -118,9 +118,6 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
     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) {
@@ -147,7 +144,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
                         throw ule;
                     }
                 }
-
+                logger.info("Using vectorized implementation of PairHMM");
                 isVectorLoglessPairHMMLibraryLoaded = true;
                 jniInitializeClassFieldsAndMachineMask(JNIReadDataHolderClass.class, JNIHaplotypeDataHolderClass.class, enableAll);        //need to do this only once
             }

public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc

@@ -53,7 +53,7 @@ LoadTimeInitializer::LoadTimeInitializer()		//will be called when library is loa
   //Function: enabling FTZ converts denormals to 0 in hardware
   //Denormals cause microcode to insert uops into the core causing big slowdown
   _MM_SET_FLUSH_ZERO_MODE(_MM_FLUSH_ZERO_ON);
-  cout << "FTZ enabled - may decrease accuracy if denormal numbers encountered\n";
+  //cout << "FTZ enabled - may decrease accuracy if denormal numbers encountered\n";
 #else
   cout << "FTZ is not set - may slow down performance if denormal numbers encountered\n";
 #endif