--- a/sirius_csifingerid.py	Wed Feb 02 17:29:46 2022 +0000
+++ b/sirius_csifingerid.py	Fri Feb 04 10:09:40 2022 +0000
@@ -390,16 +390,18 @@
                 ad = paramds[fn.split(os.sep)[-2]]['additional_details']
 
                 for line in reader:
-                    if 'rank' in line and \
-                            0 < int(rank_filter) < int(line['rank']):
+                    if 'rank' in line \
+                            and 0 < int(rank_filter) < int(line['rank']):
                         # filter out those annotations greater than rank filter
                         # If rank_filter is zero then skip
                         continue
 
-                    if 'ConfidenceScore' in line \
-                            and 0 < int(confidence_filter) < int(line['rank']):
-                        # filter out those annotations greater than rank filter
-                        # If rank_filter is zero then skip
+                    if ('ConfidenceScore' in line
+                        and 0 < float(confidence_filter)
+                        and float(line['ConfidenceScore']) <
+                            float(confidence_filter)):
+                        # filter out those annotations that are less than
+                        # the confidence filter value
                         continue
                     line.update(ad)
 
@@ -414,13 +416,13 @@
         os.system(s2)
 
 
-concat_output('canopus_summary.tsv',
-              args.canopus_result_pth,
+concat_output('compound_identifications.tsv',
+              args.annotations_result_pth,
               args.rank_filter,
               args.confidence_filter,
               args.backwards_compatible)
-concat_output('compound_identifications.tsv',
-              args.annotations_result_pth,
+concat_output('canopus_summary.tsv',
+              args.canopus_result_pth,
               0,
               0,
               False)