Now processTagged return CPM normalized read counts

src/processTagged.cpp

@@ -285,7 +285,17 @@ inline void process_file(taggedInputFile& input_file, std::unordered_map<std::st
 
     // Transfer the results from the temp data structure to the full data structure
     results_mutex.lock();
-    for (auto marker : temp_results) results[marker.first][input_file.individual_name] += marker.second;
+    //CPM normalization
+    double nbreads = 0;
+    for (auto marker : temp_results) {
+        nbreads += marker.second;
+    }
+    
+    double permillion = nbreads/1000000;
+
+    for (auto marker : temp_results) {
+        results[marker.first][input_file.individual_name] += round(marker.second / permillion);
+    }
     results_mutex.unlock();
 
     log("Finished processing individual " + input_file.individual_name + " trimmed tag " + tag + " and "+ std::to_string(maxtagl - tagl)+ " bases in the tail for loci" + input_file.path );