Finish PoC joint-probility assembler + variant caller by passing my polished graphs into pggb/odgi+vg variant deconvolution flow

[cjprybol]

algorithm:

• deconvolve reads into kmer graph
• iterative correction, starting at first k-length with sparsity, ending at first k-length with no updates (possibly better terminating conditions, should look into that)
• write graph out as GFA (try compacted and raw)
• to determine primary contigs using shortest path with L = (1 / total bases, where total bases = length * average depth or the actual lossless alignment calculation), or to start but with external dependencies, add try metaflye or https://github.com/lh3/minigraph
• use primary contigs as reference for generating variant calls using ODGI -> VG flow, or possibly VG directly
• ensure that VG variant calling can use coverage information - if not, update VCF files with depth-of-coverage information https://odgi.readthedocs.io/en/latest/rst/commands/odgi_build.html

[cjprybol]

cc @aeronth

[cjprybol]

complete