Refactored code

Author: nkongenelly

checkQC/parsers/illumina.py

@@ -79,7 +79,7 @@ def from_bclconvert(cls, runfolder_path, parser_config):
                         sample_summary := index_summary.at(lane).at(sample_no)
                     ).sample_id(),
                     "cluster_count": sample_summary.cluster_count(),
-                    "percent_of_lane":next(
+                    "percent_of_lane": next(
                         round(float(sample_stat["% Reads"]) * 100, 2)
                         for sample_stat in demultiplex_stats
                         if sample_stat["Lane"] == str(lane + 1) and
@@ -100,7 +100,7 @@ def from_bclconvert(cls, runfolder_path, parser_config):
                         )
                     ),
                     "percent_q30": next(
-                        float(row["% Q30"])
+                        float(row["% Q30"]) * 100
                         for row in quality_metrics
                         if (
                             row["Lane"] == str(lane + 1)

tests/test_qc_data.py

@@ -124,15 +124,15 @@ def bclconvert_runfolder():
                         "percent_of_lane": 0.29,
                         "percent_perfect_index_reads": 97.96,
                         "mean_q30": 36.37,
-                        "percent_q30": 0.96,
+                        "percent_q30": 96,
                     },
                     {
                         "sample_id": "Sample_14575-Qiagen-IndexSet1-SP-Lane1",
                         "cluster_count": 8560,
                         "percent_of_lane": 0.25,
                         "percent_perfect_index_reads": 98.15,
                         "mean_q30": 36.43,
-                        "percent_q30": 0.96,
+                        "percent_q30": 96,
                     },
                 ],
             },
@@ -196,15 +196,15 @@ def bclconvert_runfolder():
                         "percent_of_lane": 0.3,
                         "percent_perfect_index_reads": 98.2,
                         "mean_q30": 36.4,
-                        "percent_q30": 0.96,
+                        "percent_q30": 96,
                     },
                     {
                         "sample_id": "Sample_14575-Qiagen-IndexSet1-SP-Lane2",
                         "cluster_count": 8672,
                         "percent_of_lane": 0.25,
                         "percent_perfect_index_reads": 98.29,
                         "mean_q30": 36.48,
-                        "percent_q30": 0.97,
+                        "percent_q30": 97,
                     },
                 ],
             },