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Feature request: Add `--output-format` flag #380

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nylander opened this issue Apr 25, 2019 · 2 comments

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@nylander
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commented Apr 25, 2019

Hi,
I was trying to get cutadapt to print fasta format to stdout, but since the output is auto-detected from the file suffix of the output file, I could not find a way.

A possible solution is to add a new option, --output-format, or similar, to override the automatic (filename-based) setting? Could potentially be very useful:

cutadapt  [other options]  --output-format=fasta  input.fastq  |  \
    [some downstream analyses on fasta format]

Cheers
Johan

@marcelm marcelm closed this in 776fb88 Jun 10, 2019

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commented Jun 10, 2019

I’ve now added an option named --fasta. I started with --output-format at first, but then realized that this would introduce too many sources of errors, in particular I would have to check whether --output-format=fastq is used although the input is FASTA. When I implement more output formats, I can still add --output-format.

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commented Jun 10, 2019

The option only influences the format of the data that gets written to standard output, everything else (for which file names need to be provided anyway) is still detected based on the file name.

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