Michael Hall

FWIW I just used this SAM file for the first time to debug some things and it was super helpful in its current form.

@leoisl given you are working on `index` at the moment maybe it makes sense for you to add this in?

I would also add to this that the current subsetting is channel biased. To elaborate: the fastq files output by the basecaller are grouped by channel, in 4000 reads/fastq. So...

> I dislike automatic stdin/stdout selection though and think the existing unix standard of "-" is sufficient. I also dislike "-i" as it's non-standard and think it was a mistake...

You can only "normalise" the variant positions in the VCF to a reference genome if the `--vcf-ref` argument was used. Here is an example of a script I use to...

> It seems like a --vcf-ref is not an ordinary fasta file. So I cant use one of my genomes as a reference? What are your PRGs? Genes? If so,...

The best solution here could be an option to create a file with mapping coordinates for each read. I *think* we already print this in the debug log, so it...

I'm not saying we print out something that says mapped or unmapped. If we provide the read and its mapping coordinates (a line for each set of coordinates - so...

I guess we're converging on GAM (VGs version of BAM that I can't find any specs for)

That seems like a sane approach to me. I used a similar (slightly more naive) approach when evaluating the very first iteration of denovo discovery.