Single command haplotype sampling

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• Added vg giraffe --haplotype-sampling to automatically count kmers and haplotype-index and haplotype-sample the graph. Make sure to have kmc installed. Providing either a --kff-name or --haplotype-name will now also trigger generation of the other. To do one-reference sampling, continue to use --set-reference. To do non-diploid sampling with a certain number of haplotypes, use --no-diploid-sampling and --num-haplotypes.

Description

This allows Giraffe to be used as a single-command haplotype sampling workflow, without needing separate commands to count kmers, haplotype-index the graph, haplotype-sample the graph, and map.

I introduced a notion of "scopes" for indexes in the registry, so I could attach a scope of the sample name to the FASTQ or KFF and have it propagate and qualify/subscript all indexes that depend on them. This works OK, but to get the "right" filenames we'd been using for the sampled GBZ (<prefix>.<sample>.gbz), when it's doubling as a "Giraffe GBZ", I've had to introduce a notion of multiple possible extensions for an index, and then a bunch of logic to work out which of the extensions we actually should use so we don't conflict with older things in the plan.

I think I might be able to replace all that with a notion of "weak" aliases, so the "Giraffe GBZ" can come from the "Haplotype-Sampled GBZ" but use it at the "Haplotype-Sampled GBZ"'s name instead of its own.

[adamnovak]

I don't think the "weak" alias approach would work unless the haplotype-sampled GBZ knew it was always sample-scoped and always had {sample}.gbz as its suffix, with some notion of a wildcard. Otherwise we would think it would try and fight the plain GBZ for the gbz suffix.

[adamnovak]

I haven't done weak aliases, but I've made the scopes keyed (so we know we're dealing with a scope for "sample"), and I've introduced Snakemake-style {} wildcards in the extensions. We now pick the first extension where we have all the wildcards available as scopes, so we use {sample}.gbz for the Giraffe GBZ when we can and giraffe.gbz otherwise.