diff --git a/deepconsensus/quality_calibration/filter_reads.py b/deepconsensus/quality_calibration/filter_reads.py index 90eef6e..a326475 100644 --- a/deepconsensus/quality_calibration/filter_reads.py +++ b/deepconsensus/quality_calibration/filter_reads.py @@ -28,6 +28,7 @@ # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. """Filter reads based on the base qualities.""" +from collections.abc import Sequence import math from absl import app from absl import flags @@ -64,7 +65,7 @@ def register_required_flags(): 'quality_threshold']) -def avg_phred(base_qualities: list[float]) -> float: +def avg_phred(base_qualities: Sequence[float]) -> float: """Get the average phred quality given base qualities of a read. Args: diff --git a/docs/quick_start.md b/docs/quick_start.md index a16e44e..41f0a92 100644 --- a/docs/quick_start.md +++ b/docs/quick_start.md @@ -303,8 +303,8 @@ deepconsensus run \ At the end of your run, you should see: ``` -Processed 178 ZMWs in 230.602 seconds -Outcome counts: OutcomeCounter(empty_sequence=0, only_gaps=0, failed_quality_filter=1, failed_length_filter=0, success=177) +Processed 178 ZMWs in 234.950 seconds +Outcome counts: OutcomeCounter(empty_sequence=0, only_gaps=0, failed_quality_filter=2, failed_length_filter=0, success=176) ``` ## Optimizing Runtime