progression print

partitioning/fast_clustering_t.cpp

@@ -87,6 +87,9 @@ void process_file_part(const std::string& input_filename, int part_id, int start
     // Process the lines in the file part
     std::string read_name;
     std::string sequence;
+    int read_count = 0;
+    int total_reads = (end_line - start_line)/4;
+    int step_count = 0;
 
     // process the lines in the file part, add 4 lines to the i counter each loop
     for (int i = start_line; i < end_line; i+=4) {
@@ -104,6 +107,14 @@ void process_file_part(const std::string& input_filename, int part_id, int start
         // find the position fo the primer and get the bases following it
         std::string cluster_id = get_cluster_id(sequence, seq_to_find, split_level);
 
+        read_count += 1;
+
+        if (read_count >= total_reads/10 && part_id == 0){
+            read_count = 0;
+            step_count += 1;
+            std::cout << "thread " << part_id << " : " << step_count <<"0%" << std::endl;
+        }
+
         if (cluster_id == "None") {
             continue; // ignore the read
         }
@@ -118,6 +129,7 @@ void process_file_part(const std::string& input_filename, int part_id, int start
             return;
         }
         output_file << ">" << read_name << "\n" << sequence << "\n";
+
     }
 }