[WIP] explore all overlapping genomes, not just minimum metagenome cover

[ctb]

This PR explores the prefetch results (containing all overlapping genomes), as a way of beginning to evaluate strain specificity of the minimum metagenome cover.

Specifically,

• adds a target map_prefetch that maps the sample reads to all overlapping genomes, not just the minimum set;
• adds variant calling and SNP estimation in order to look at variation rates (incl ANI) between the metagenome and its various reference genomes.

relevant: #18

Next things to do -

• support config-file-based selection of taxonomic clades for prefetch investigation; without this, all the found genbank genomes would be mapped (so, e.g. 200,000 salmonella genomes 😆 ) Note to self: we should be able to do this with picklists support a picklist in the config file #132, being added in [MRG] support local genome collections (including private genomes) #130
• pair this with a taxonomic summary (at fixed level like genus, or something?) of prefetch results

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variant calling on gather results

The SNP stuff is already pretty illuminating -- as expected, most but not all of the mock community members have very few SNPs, while the real communities ...do.

podar mock

zymo mock

human gut real

oil well real