How does one set the mismatch, deletion settings?

[rgranit]

I've looked at the documentation and could not find how does one define the amount or allowed mismatches and deletions.. any advice?

Thanks!

[jfjlaros]

To allow for insertions or deletions (disabled by default) the -d option should be used. The amount of mismatches (including insertions and deletions, if enabled) is controlled with the -m option.

Interestingly, this is indeed not described in the documentation, I will add it. Thank you for pointing this out.

[rgranit]

Thanks! adding this to the documentation would be great. Also when you run demultiplex --help it does not suggest these options.

[jfjlaros]

That is because these options are specific for the subcommands demux and match. E.g., when you run demultiplex demux -h, you should get a full list of options relevant for that subcommand.

[jfjlaros]

Fixed in 4099984921d42c4a141c06c13e496ff633f6b92e.