Fix deepconsensus filter_reads cli.

PiperOrigin-RevId: 513036217
google · Feb 28, 2023 · 82df652 · 82df652
1 parent 7dd3bb0
commit 82df652
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git 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
@@ -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