use cerr rather than cout everywhere

src/BuildSalmonIndex.cpp

@@ -117,8 +117,8 @@ Index
 ==========
 Creates a salmon index.
 )";
-            std::cout << hstring << std::endl;
-            std::cout << generic << std::endl;
+            std::cerr << hstring << std::endl;
+            std::cerr << generic << std::endl;
             std::exit(0);
         }
         po::notify(vm);

src/Salmon.cpp

@@ -75,7 +75,6 @@ int help(int argc, char* argv[]) {
     */
 
     std::cerr << helpMsg.str();
-//std::cerr << "    Salmon v" << salmon::version << helpmsg << "\n";
     return 1;
 }
 
@@ -176,7 +175,6 @@ int main( int argc, char* argv[] ) {
     }
 
     if (vm.count("help") and !vm.count("command")) {
-        //std::cout << sfopts << std::endl;
         help(argc, argv);
         std::exit(0);
     }

src/SalmonQuantify.cpp

@@ -2293,8 +2293,8 @@ Quant
 Perform streaming mapping-based estimation of
 transcript abundance from RNA-seq reads
 )";
-      std::cout << hstring << std::endl;
-      std::cout << visible << std::endl;
+      std::cerr << hstring << std::endl;
+      std::cerr << visible << std::endl;
       std::exit(0);
     }
 

src/SalmonQuantifyAlignments.cpp

@@ -1349,8 +1349,8 @@ int salmonAlignmentQuantify(int argc, char* argv[]) {
         po::store(orderedOptions, vm);
 
         if (vm.count("help")) {
-            std::cout << "Salmon quant (alignment-based)\n";
-            std::cout << visible << std::endl;
+            std::cerr << "Salmon quant (alignment-based)\n";
+            std::cerr << visible << std::endl;
             std::exit(0);
         }
         po::notify(vm);
@@ -1485,7 +1485,7 @@ int salmonAlignmentQuantify(int argc, char* argv[]) {
             std::exit(1);
         }
 	if (!sopt.quiet) {
-	  std::cout << "Logs will be written to " << logDirectory.string() << "\n";
+	  std::cerr << "Logs will be written to " << logDirectory.string() << "\n";
 	}
 
         bfs::path logPath = logDirectory / "salmon.log";

src/SalmonUtils.cpp

@@ -1322,7 +1322,7 @@ bool processQuantOptions(SalmonOpts& sopt,
   }
 
   if (!sopt.quiet) {
-    std::cout << "Logs will be written to " << logDirectory.string() << "\n";
+    std::cerr << "Logs will be written to " << logDirectory.string() << "\n";
   }
 
   // Determine what we'll do with quasi-mapping results