Properly report error when two contigs both pass.

cfe-lab · Jun 7, 2021 · db92888 · db92888
1 parent 4bd76cc
commit db92888
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/gene_splicer/outcome_summary.py b/gene_splicer/outcome_summary.py
@@ -34,11 +34,15 @@ def add_sample(self, row):
         }
 
     def set_passed(self, row):
+        seqtype = row['seqtype']
+        if seqtype.endswith('s'):
+            seqtype = seqtype[:-1]
+        passed_field = seqtype + '_passed'
         self.data[row['sample']]['reference'] = row['reference']
         self.data[row['sample']]['seqlen'] = row['seqlen']
-        self.data[row['sample']]['conseq_passed'] = True
+        self.data[row['sample']][passed_field] = True
         self.data[row['sample']]['sequence'] = row['sequence']
-        self.data[row['sample']]['seqtype'] = row['seqtype']
+        self.data[row['sample']]['seqtype'] = seqtype
         self.data[row['sample']]['is_rev_comp'] = row['is_rev_comp']
 
     def set_failed(self, row, error):