qc: add heteroplasmy scan, spectrum and per-molecule phasing tools

samtools mpileup allele counts per strand, heteroplasmic site calling with hotspot,
homopolymer, cross-talk and two-individual mixture flags, substitution spectrum with
depth-adjusted group tests, and Fisher-based phasing of minor alleles on the same
molecules from per-read bases. First run on the rescued human blood and Letizia sets
is recorded in docs/pipeline_notes.md#numt_rescue: two run04 controls are mixtures of
two individuals; the mice match the C57BL/6J reference with no callable heteroplasmy.

Co-Authored-By: Claude Fable 5.1 <[email protected]>