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when using --revcomp, allow to configure the addition of the " rc" string in the header

See original GitHub issue

Hello, Using cutadapt 2.10 with Python 3.6.9, when using the --revcomp argument, the program appends an rc string to identify the sequence on which the primers were found in the reverse complement. This is documented in the docs: https://cutadapt.readthedocs.io/en/stable/guide.html#searching-reverse-complements

The name of a reverse-complemented read is changed by adding a space and rc to it. (Please file an issue if you would like this to be configurable.)

So I would like to be the one that makes that request to add an option to control if the string is added or not. The reason is that I’m using custom files which I filled with some taxonomic information in the header, causing this extra string to be treated like a subspecies in my flow. The workaround is to open the output file just to remove the string, but it would be great if there were an option where the string is not added in the first place.

Best regards and thanks for such a great tool!

Issue Analytics

  • State:closed
  • Created 3 years ago
  • Comments:12 (7 by maintainers)

github_iconTop GitHub Comments

1reaction
marcelmcommented, Mar 4, 2021

I’ve added the {rc} template variable now

1reaction
fjossandoncommented, Jan 29, 2021

Awesome! I just tested the development version and it works perfectly: >example_reverse_complement prefix description 2 suffix =) Thanks for your hard work!

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