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Update cli.py #793

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6 changes: 4 additions & 2 deletions src/cutadapt/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1105,11 +1105,13 @@ def make_adapter_cutter(
def make_shortener(length1: Optional[int], length2: Optional[int], paired: bool):
if paired:
if length1 is not None and length2 is not None:
# If -l and -L are given, shorten both reads.
yield Shortener(length1), Shortener(length2)
elif length1 is not None and length2 is None:
# If -L not given, use same setting for both
yield Shortener(length1), Shortener(length1)
# If only -l is given, shorten read 1.
yield Shortener(length1), None
elif length1 is None and length2 is not None:
# If only -L is given, shorten read 2.
yield None, Shortener(length2)
else:
if length1 is not None:
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