Add counts of different alleles at each site in each sample in a reference free alignment

[Gerry Tonkin-Hill]

[Simon Harris]

SKA doesn't have that information at that stage, but I could output it from ska fastq and provide a way to look up allele frequencies based on a set of split kmers. Would that work?

[Gerry Tonkin-Hill]

Yeah that would be great! It would be very helpful for any within-host mixed sample analysis.

[Simon Harris]

I've added the option to output allele counts during ska fastq and also ska humanise to output kmers in a human readable format (with the middle bases of each sample). You should be able to use the first column from that to find your allele frequencies in the allele count files.