Module commands 

CLI subcommand implementations for the holodeck binary.

Each subcommand lives in its own module and implements the command::Command trait. common holds the shared CLI option groups (--reference, output, VCF, BED, seed) flattened into every subcommand. simulate drives the read-simulation pipeline; mutate produces random variant VCFs; eval scores alignment accuracy; methylate builds the methylation-truth VCF consumed by simulate’s bisulfite / TAPS chemistry.

Modules

command

common

eval

Alignment accuracy evaluation command.

methylate

methylate subcommand — generate per-haplotype CpG methylation truth as an MT/MB-annotated VCF, optionally writing a population-fraction bedGraph. methylate subcommand — given a reference (and optional variant VCF), produce a methylation-annotated VCF that records per-haplotype per-strand methylation state at every CpG.

mutate

simulate