Extends the entropy annex pipeline to optionally compute family overlap data in a single pass, introducing a memory-mapped binary format and an in-memory accumulator for efficient storage. Adds --min-shared-family to auto-exclude genomes below a threshold during SNP-family distance computation, and --family-overlap to export a shared family matrix as CSV. Centralizes upper-triangle indexing into a shared helper function to eliminate duplication.
Eric Coissac
e101f629e6