Skip to content

Commit

Permalink
feat(count all reads of negative controls) (#3682)(patch)
Browse files Browse the repository at this point in the history
### Added

- Condition to account for all reads for negative control samples regardless of q30.
  • Loading branch information
beatrizsavinhas authored Sep 4, 2024
1 parent 48dcb0f commit 1708175
Showing 1 changed file with 4 additions and 1 deletion.
5 changes: 4 additions & 1 deletion cg/store/crud/update.py
Original file line number Diff line number Diff line change
Expand Up @@ -68,7 +68,10 @@ def update_sample_reads_illumina(self, internal_id: str, sequencer_type: Sequenc
q30_threshold: int = get_q30_threshold(sequencer_type)

for sample_metric in sample_metrics:
if sample_metric.base_passing_q30_percent >= q30_threshold:
if (
sample_metric.base_passing_q30_percent >= q30_threshold
or sample.is_negative_control
):
total_reads_for_sample += sample_metric.total_reads_in_lane

sample.reads = total_reads_for_sample
Expand Down

0 comments on commit 1708175

Please sign in to comment.