calculate thread number better

src/SalmonAlevin.cpp

@@ -1826,11 +1826,8 @@ void sc_align_read_library(ReadExperimentT& readExp,
     size_t numFiles = rl.mates1().size() + rl.mates2().size();
     uint32_t numParsingThreads{1};
     // HACK!
-    // below ~6 threads, assume that parser won't do
-    // too much actual cpu work.
-    if(numThreads > 6){
-      numThreads -= 1;
-    }
+    // if we have more than 1 set of input files and the thread count is 
+    // greater than 8, then dedicate a second thread to parsing.
     if (rl.mates1().size() > 1 and numThreads > 8) { numParsingThreads = 2; numThreads -= 1;}
     pairedParserPtr.reset(new paired_parser(rl.mates1(), rl.mates2(), numThreads, numParsingThreads, miniBatchSize));
     pairedParserPtr->start();
@@ -2562,6 +2559,13 @@ int alevin_sc_align(AlevinOpts<ProtocolT>& aopt,
 
     sopt.allowOrphans = true;
     sopt.useQuasi = true;
+
+    // lose one thread for parsing
+    // TODO: is it reasonable to assume 
+    // that the work done by the parsing thread
+    // will be substantial enough to count if 
+    // the remaining mapping thread count is 
+    // too small?
     if(sopt.numThreads > 1){
       sopt.numThreads -= 1;
     }