barcode_correction.py: modified mapping quality setting of reads with…

… more than 3 mismatches
imgag · Jun 15, 2023 · ebe0d57 · ebe0d57
1 parent 4db3ee8
commit ebe0d57
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/barcode_correction.py b/barcode_correction.py
@@ -168,8 +168,8 @@ def consensus_quality(qualities, min_bq, errors):
         new_qual = max_qual
 
     else:
-        # Unreliable consensus labeled with quality 0: if 3 or more discordant bases, or more than 25% discordant bases
-        if (errors >= 1 and float(errors) / (copies + errors) > 0.25) or errors >= 3:
+        # Unreliable consensus labeled with quality 0: if more than 25% discordant bases
+        if (errors >= 1 and float(errors) / (copies + errors) > 0.25):
             new_qual = 0
 
         # Otherwise, the maximum quality value across PCR copies is used as new quality, with minimum of 30