holodeck_lib/commands/mod.rs
1//! CLI subcommand implementations for the `holodeck` binary.
2//!
3//! Each subcommand lives in its own module and implements the [`command::Command`]
4//! trait. [`common`] holds the shared CLI option groups (`--reference`, output,
5//! VCF, BED, seed) flattened into every subcommand. `simulate` drives the
6//! read-simulation pipeline; `mutate` produces random variant VCFs; `eval`
7//! scores alignment accuracy; `methylate` builds the methylation-truth VCF
8//! consumed by `simulate`'s bisulfite / TAPS chemistry.
9
10pub mod command;
11pub mod common;
12pub mod eval;
13/// `methylate` subcommand — generate per-haplotype CpG methylation truth
14/// as an MT/MB-annotated VCF, optionally writing a population-fraction bedGraph.
15pub mod methylate;
16pub mod mutate;
17pub mod simulate;