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jhhung / PEAT

An ultra fast and accurate paired-end adapter trimmer that needs no a priori adapter sequences.
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Allow user to choose output R1 and R2 files (again) #18

Closed tseemann closed 9 years ago

tseemann commented 9 years ago

I have tried the new --output_1 option you said you added in https://github.com/jhhung/PEAT/issues/5 However, it does not do what was requested.

If I do --output_1 R1.trimmed.fq I still get a file R1.trimmed.fq_paired1.fq. Why does it have the _paired1.fq on the end?

I can use -o if I want a prefix.

RalfHsiao commented 9 years ago

We fixed the problem and update the PEATv1.1 in release. Thank you your advice.

tseemann commented 9 years ago

You still need to fix the --help ?

  --output_1 arg (=stdout)             Prefix for Output file part1 name,
                                       stdout by default
  --output_2 arg (=stdout)             Prefix for Output file part2 name,
                                       stdout by default