Added index positions (#113)

* Differentiated indexed read values from non-indexed reads

* Refactor code

* Refactored code

checkQC/__init__.py

@@ -1,2 +1,2 @@
 
-__version__ = "4.0.1"
+__version__ = "4.0.2-rc1"

checkQC/handlers/q30_handler.py

@@ -28,12 +28,18 @@ def collect(self, signal):
 
     def check_qc(self):
 
+        index_count = 0
+        non_index_count = 0
         for error_dict in self.error_results:
             lane_nbr = int(error_dict["lane"])
-            read = error_dict["read"]
             percent_q30 = error_dict["percent_q30"]
-            is_index_read = error_dict["percent_q30"]
+            is_index_read = error_dict.get("is_index_read", False)
             read_or_index_text = "index read" if is_index_read else "read"
+            # Differentiate read values for indexed from non-indexed reads
+            index_count += 1 if is_index_read else 0
+            non_index_count += 1 if not is_index_read else 0
+
+            read = index_count if is_index_read else non_index_count
 
             if self.error() != self.UNKNOWN and percent_q30 < self.error():
                 yield QCErrorFatal(

tests/handlers/test_q30_handler.py

@@ -27,7 +27,7 @@ def test_all_is_fine(self):
         self.set_qc_config(qc_config)
         errors_and_warnings = list(self.q30_handler.check_qc())
         self.assertIn("index read", f"{errors_and_warnings}")
-        self.assertEqual(f"{errors_and_warnings}", "[Fatal QC error: %Q30 50.00 was too low on lane: 1 for index read: 3]")
+        self.assertEqual(f"{errors_and_warnings}", "[Fatal QC error: %Q30 50.00 was too low on lane: 1 for index read: 1]")
 
     def test_warning(self):
         qc_config = {'name': 'Q30Handler', 'error': 70, 'warning': 85}