Reverse qual if reverse complementing read

WEHIGenomicsRnD · Jun 18, 2024 · 0ec414a · 0ec414a
1 parent be8fc4e
commit 0ec414a
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/bin/trim_primer.py b/bin/trim_primer.py
@@ -61,6 +61,7 @@ def parse_args():
 
 def trim_read(read_seq, read_qual, fwd_primer, rev_primer, mismatches, barcode_length, rc_read=False):
  read_seq = rc(read_seq) if rc_read else read_seq
+ read_qual = read_qual[::-1] if rc_read else read_qual
  fwd_result = edlib.align(fwd_primer, read_seq, mode="HW", task="path", k=mismatches)
  rev_result = edlib.align(rev_primer, read_seq, mode="HW", task="path", k=mismatches)