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 9d46dac80..15195728b 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 @@ -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 } diff --git a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc b/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc index 52accef3d..f6cdbab4b 100644 --- a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc +++ b/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 diff --git a/public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so b/public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so index ca0f6eef7..2a55b7b0f 100644 Binary files a/public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so and b/public/sting-utils/src/main/resources/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so differ