Module vcf 

VCF input/output for holodeck.

Reads variants from a multi-sample VCF (resolving GT against a chosen sample) for use by simulate and methylate, and houses the methylation classifier and MT/MB FORMAT reader/writer that carries per-haplotype per-strand CpG methylation truth between the two commands. Submodules:

• genotype — Genotype and VariantRecord types plus GT parsing.
• methylation — per-CpG classifier, MT/MB writer/reader, and header probe.

Modules

genotype

methylation

Per-CpG methylation classifier and MT/MB FORMAT VCF reader/writer used by the methylate subcommand and the methylation-aware simulate path. VCF MT/MB FORMAT-field schema, per-CpG ownership classifier, and reader/writer for methylation-annotated VCFs.

Structs

ParsedVariants

Result of a single-pass VCF scan: per-contig ALT-bearing variants plus the sample’s ploidy resolved from unfiltered genotypes.

Functions

parse_variants_by_contig

Read every variant from a VCF in a single pass and partition by contig.