Suggestion: warn that modkit pileup doesn't accept gzip-ed reference

[CLeib]

Hi,

When running modkit pileup with a reference fasta I kept getting the message "fetching sequence failed, got illegal characters in sequence" for each read. It took me a while to figure out that the reason for that is that a fa.gz reference is not handled correctly.
I'd like to suggest that the program give a warning at the beginning of the run if the file format is not correct, or even just add a warning to the user guide (especially since some other nanoporetech programs do accept fa.gz files).

Hope you'll take this into consideration, Thanks, Chen

[ArtRand]

I agree. Also allowing .gz references is probably a good idea.

[xscapintime]

Same here