Patch comparison for q30 threshold (#424)(patch)

### Fixed - Q30 score values used in sequencing QC functions.
Clinical-Genomics · Aug 17, 2023 · 53474b2 · 53474b2
1 parent 357392a
commit 53474b2
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/cg_lims/EPPs/qc/sequencing_quality_checker.py b/cg_lims/EPPs/qc/sequencing_quality_checker.py
@@ -63,7 +63,7 @@ def _update_sample_with_quality_results(
             sample_id=metrics.sample_internal_id,
             lane=metrics.flow_cell_lane_number,
             reads=metrics.sample_total_reads_in_lane,
-            q30_score=metrics.sample_base_fraction_passing_q30,
+            q30_score=metrics.sample_base_fraction_passing_q30 * 100,
             passed_quality_control=passed_quality_control,
         )
 
@@ -75,7 +75,7 @@ def _quality_control(self, metrics: SampleLaneSequencingMetrics) -> bool:
 
     def _passes_quality_thresholds(self, q30_score: float, reads: int) -> bool:
         """Check if the provided metrics pass the minimum quality thresholds."""
-        passes_q30_threshold = q30_score >= self.q30_threshold
+        passes_q30_threshold = q30_score * 100 >= self.q30_threshold
         passes_read_threshold = reads >= self.READS_MIN_THRESHOLD
         return passes_q30_threshold and passes_read_threshold
 

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -289,7 +289,7 @@ def novaseq_metrics_passing_thresholds_json(
         sample_ids=novaseq_sample_ids,
         lanes=novaseq_lanes,
         total_reads_in_lane=10000,
-        base_fraction_passing_q30=100,
+        base_fraction_passing_q30=0.95,
     )
 
 
@@ -315,7 +315,7 @@ def novaseq_metrics_failing_reads_json(
         sample_ids=novaseq_sample_ids,
         lanes=novaseq_lanes,
         total_reads_in_lane=0,
-        base_fraction_passing_q30=100,
+        base_fraction_passing_q30=0.95,
     )
 
 
@@ -328,7 +328,7 @@ def novaseq_metrics_two_failing(
         sample_ids=novaseq_sample_ids,
         lanes=novaseq_lanes,
         total_reads_in_lane=10000,
-        base_fraction_passing_q30=100,
+        base_fraction_passing_q30=0.95,
     )
 
     metrics[0]["sample_base_fraction_passing_q30"] = 0
@@ -365,7 +365,7 @@ def novaseq_metrics_missing_for_sample_in_lane(
         sample_ids=novaseq_sample_ids,
         lanes=novaseq_lanes,
         total_reads_in_lane=10000,
-        base_fraction_passing_q30=100,
+        base_fraction_passing_q30=0.95,
     )
     for metric in metrics:
         if (
@@ -390,7 +390,7 @@ def novaseq_missing_sample(
         sample_ids=novaseq_sample_ids,
         lanes=novaseq_lanes,
         total_reads_in_lane=10000,
-        base_fraction_passing_q30=100,
+        base_fraction_passing_q30=0.95,
     )
     return metrics