Cancer simulation

eidolon simulates tumor / normal sequencing data end-to-end. The eidolon gen-cancer-reads -c <config.yml> subcommand runs two gen-reads passes — one normal-genotype, one tumor — over the same reference and merges them at a configurable purity into a single “tumor biopsy” FASTQ that downstream somatic callers (Mutect2, Strelka, Manta, …) consume directly, plus an origin-tagged truth VCF (INFO/EIDOLON_ORIGIN ∈ {germline, somatic, shared}) for scoring. It also generates the foundational structural-variant types cancer SVs depend on — <BND> translocations, <INV> inversions, and de novo <INS> — and ships bundled pan-cancer and per-tissue (BRCA / skin / lung) models plus Docker-based benchmark pipelines.

See docs/cancer_howto.md for a copy-paste guide with worked examples, output reference, benchmarking, and model training. Design rationale and calibration caveats live in docs/cancer_simulator.md.