Marco Galardini

I think this is due to the fact that we do not really expect missing values in an .Rtab file, whereas they can be quite common in vcf files. I...

Ok that makes sense. If you would like to open a PR we could merge this change. If you know how to add unit tests that would also be great....

Hi, which version of pyseer are you using? Try `pyseer --version`. Also, can you paste here the output of the following command: `mash dist mash_sketch.msh mash_sketch.msh | head` Thanks On...

And can you paste here the output of `mash dist mash_sketch.msh mash_sketch.msh | head`?

Can't see anything wrong at a first glance; perhaps you have one of the filenames with the fasta sequences with a space in its name?

Thanks for the PR; maybe making a new Rtab file with missing values and making sure those are handled correctly in an ad-hoc unit test? Happy to prepare it if...

Thanks, I'll review the changes shortly and merge. I checked again and we do ignore the samples with missing values (see here: https://github.com/mgalardini/pyseer/blob/1359b614491bca96264d9bd8e6535ec90a3cbedf/pyseer/input.py#L427). I think we may want to assume...

Ah wait I think we might have had a misunderstanding (my fault really!). How we handle missing variants in VCF files is a bit convoluted because we have to handle...

Hi, you can follow the tutorial for some hints into doing what you describe (i.e. annotating your hits): [interpreting significant k-mers](https://pyseer.readthedocs.io/en/master/tutorial.html#interpreting-significant-k-mers). You want to look into the `annotate_hits_pyseer` command, optionally...

Are you sure you have a recent version of pyseer? [You can download the latest one](https://github.com/mgalardini/pyseer/releases/tag/1.3.11), for which the option should be available. Another thing to mention is that you...