Messages that were going to stdout now going to stderr

Make PairHMM outputs go to stderr instead of stdout

Change output from stdout to stderr in close()

Updated lib with output going to stderr

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

@@ -264,7 +264,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
     @Override
     public void close() {
         if (doProfiling)
-            System.out.println("Time spent in setup for JNI call : " + (pairHMMSetupTime * 1e-9));
+            System.err.println("Time spent in setup for JNI call : " + (pairHMMSetupTime * 1e-9));
         super.close();
         jniClose();
     }

public/VectorPairHMM/src/main/c++/Sandbox.java

@@ -156,7 +156,7 @@ public class Sandbox {
     public native void jniClose();
     public void close()
     {
-        System.out.println("Time spent in setup for JNI call : "+(setupTime*1e-9)+" compute time : "+(computeTime*1e-9));
+        System.err.println("Time spent in setup for JNI call : "+(setupTime*1e-9)+" compute time : "+(computeTime*1e-9));
         jniClose();
     }
 

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

@@ -154,20 +154,20 @@ void initialize_function_pointers(uint64_t mask)
   //mask = (1 << SSE41_CUSTOM_IDX);
   if(is_avx_supported() && (mask & (1<< AVX_CUSTOM_IDX)))
   {
-    cout << "Using AVX accelerated implementation of PairHMM\n";
+    cerr << "Using AVX accelerated implementation of PairHMM\n";
     g_compute_full_prob_float = compute_full_prob_avxs<float>;
     g_compute_full_prob_double = compute_full_prob_avxd<double>;
   }
   else
     if(is_sse41_supported() && (mask & ((1<< SSE41_CUSTOM_IDX) | (1<<SSE42_CUSTOM_IDX))))
     {
-      cout << "Using SSE4.1 accelerated implementation of PairHMM\n";
+      cerr << "Using SSE4.1 accelerated implementation of PairHMM\n";
       g_compute_full_prob_float = compute_full_prob_sses<float>;
       g_compute_full_prob_double = compute_full_prob_ssed<double>;
     }
     else
     {
-      cout << "Using un-vectorized C++ implementation of PairHMM\n";
+      cerr << "Using un-vectorized C++ implementation of PairHMM\n";
       g_compute_full_prob_float = compute_full_prob<float>;
       g_compute_full_prob_double = compute_full_prob<double>;
     }
@@ -300,16 +300,16 @@ void tokenize(std::ifstream& fptr, std::vector<std::string>& tokens)
       {
 	myVec.push_back(tmp);
 	++i;
-	//std::cout <<tmp <<"#";
+	//std::cerr <<tmp <<"#";
       }
       tmp = "";
     }
-    //std::cout << "\n";
+    //std::cerr << "\n";
     if(myVec.size() > 0)
       break;
   }
   tokens.clear();
-  //std::cout << "Why "<<myVec.size()<<"\n";
+  //std::cerr << "Why "<<myVec.size()<<"\n";
   tokens.resize(myVec.size());
   for(i=0;i<(int)myVec.size();++i)
     tokens[i] = myVec[i];
@@ -334,7 +334,7 @@ int read_mod_testcase(ifstream& fptr, testcase* tc, bool reformat)
   tc->i = new char[tc->rslen];
   tc->d = new char[tc->rslen];
   tc->c = new char[tc->rslen];
-  //cout << "Lengths "<<tc->haplen <<" "<<tc->rslen<<"\n";
+  //cerr << "Lengths "<<tc->haplen <<" "<<tc->rslen<<"\n";
   memcpy(tc->rs, tokens[1].c_str(),tokens[1].size());
   assert(tokens.size() == (size_t)(2 + 4*(tc->rslen)));
   //assert(tc->rslen < MROWS);
@@ -522,7 +522,7 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size,
           double rel_error = (baseline_result != 0) ? fabs(abs_error/baseline_result) : 0;
           if(abs_error > 1e-5 && rel_error > 1e-5)
           {
-            cout << std::scientific << baseline_result << " "<<results_vec[i]<<"\n";
+            cerr << std::scientific << baseline_result << " "<<results_vec[i]<<"\n";
             all_ok = false;
           }
         }
@@ -547,14 +547,14 @@ void do_compute(char* filename, bool use_old_read_testcase, unsigned chunk_size,
 #endif
   if(all_ok)
   {
-    cout << "All output values within acceptable error\n";
-    cout << "Baseline double precision compute time "<<baseline_compute_time*1e-9<<"\n";
+    cerr << "All output values within acceptable error\n";
+    cerr << "Baseline double precision compute time "<<baseline_compute_time*1e-9<<"\n";
   }
-  cout << "Num testcase "<<num_testcases<< " num double invocations "<<num_double_calls<<"\n";
-  cout << "Vector compute time "<< vector_compute_time*1e-9 << "\n";
+  cerr << "Num testcase "<<num_testcases<< " num double invocations "<<num_double_calls<<"\n";
+  cerr << "Vector compute time "<< vector_compute_time*1e-9 << "\n";
 #ifdef USE_PAPI
   for(unsigned i=0;i<NUM_PAPI_COUNTERS;++i)
-    cout << eventnames[i] << " : "<<accum_values[i]<<"\n";
+    cerr << eventnames[i] << " : "<<accum_values[i]<<"\n";
 #endif
 #ifdef PRINT_PER_INTERVAL_TIMINGS
   times_fptr.close();

public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java

@@ -385,6 +385,6 @@ public abstract class PairHMM {
     public void close()
     {
         if(doProfiling)
-            System.out.println("Total compute time in PairHMM computeLikelihoods() : "+(pairHMMComputeTime*1e-9));
+            System.err.println("Total compute time in PairHMM computeLikelihoods() : "+(pairHMMComputeTime*1e-9));
     }
 }