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I’ve closed #402 in favor of this issue.
Copying one of my comments:
Similar to Mothur, I’d like to implement this by searching both the read and its reverse complement for the adapter.
In your case, if the adapter was found on the reverse complement, would you like to have the reverse-complemented (and of course trimmed) sequence in the output? Or would you prefer to have it in the original orientation?
Reverse-complementing the output would be quite nice for a use case that I have because it would allow me to “normalize” the read orientation.
I will probably implement both options, but I’d like to know how to name them and with which one to start.
I could then imagine that some people would want to have an indication of whether a read has been reverse-complemented by some extra string in the header. I’m not sure how to do this. One idea is to use the
Oh, and I guess we need to count how many reads were reverse-complemented and print that in the report.
To which @koopkaup replied:
I’m working in branch
If my primers are not found on the original orientation, I would like you to try the reverse complement - and if the primers match return the trimmed reverse complement. I think @koopkaup wanted the same.
Possible API suggestions:
Or more simply: