bamfile parser skips non-unique reads.

HiLiveViral.py

@@ -419,6 +419,13 @@ def main():
         os.makedirs(os.path.join(arguments.resultfolder))
     cyclelist = sorted(set([int(x) for x in arguments.cycles]))
 
+    if not arguments.tiles:
+        print('detecting tiles')
+        arguments.tiles = detect_tiles(arguments.bcdir)
+    if not arguments.lanes:
+        print('detecting lanes')
+        arguments.lanes = detect_lanes(arguments.bcdir)
+    
     if not arguments.skip_mapping:
         # detect tiles to map
         while not os.path.isdir(os.path.join(arguments.bcdir, 'L00' + str(arguments.lanes[0]),
@@ -426,12 +433,7 @@ def main():
             print('waiting for first cycle to finish')
             time.sleep(30)
 
-        if not arguments.tiles:
-            print('detecting tiles')
-            arguments.tiles = detect_tiles(arguments.bcdir)
-        if not arguments.lanes:
-            print('detecting lanes')
-            arguments.lanes = detect_lanes(arguments.bcdir)
+
 
         # run hilive
         print('starting hilive')
@@ -477,8 +479,6 @@ def main():
             shutil.rmtree(os.path.join(arguments.resultfolder, 'output_cycle{}'.format(cycle)))
             copy_tree_structure(os.path.join(program_path, 'prelim_data'),
                                 os.path.join(arguments.resultfolder, 'output_cycle{}'.format(cycle)))
-        print(time.time() - start)
-        start = time.time()
 
         # generate tree
         print('writing data for tree')
@@ -507,8 +507,6 @@ def main():
         with multiprocessing.Pool(processes=int(arguments.threads)) as pool:
             pool.map(coverage_plot, worker_args)
 
-        print(time.time() - start)
-
 
 if __name__ == '__main__':
     main()