seqkit replace: conflict with -m flag

[kabilov]

Hi Wei,

I found one inconsistency in seqkit replace.
The flag -m is assigned to several different functions. I marked them in red in the picture.

And accordingly, the question arises about the possibility of using the --max-mismatch flag.

Best wishes,
Marsel

[shenwei356]

Dear Marsel,

Thanks for pointing this out. The help message was copied from another command :(

Yes, we can allow mismatch of sequences. But is it necessary, what's the use case?

[kabilov]

Dear Wei,

The task is somewhat specific. It is necessary to replace the pattern in many sequences. A pattern is a degenerate sequence, for example GARTCN, which must be replaced by GAATCC. But in addition, you also need to take into account possible mismatches. And if the first can be implemented through regular expressions - GA[GA]TC[GATC], then the second with mismatches is more difficult.