Module 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.

Each CpG on each haplotype is routed to exactly one VCF record by [classify_cpgs]: methylation-only records for reference-coordinate CpGs outside any variant span, and variant-record annotations for CpGs inside or straddling a variant’s alt allele.

Structs

MethylationVcfRecords

Pre-parsed methylation VCF body: header MT/MB detection plus per-contig record bytes ready for read_contig_methylation.

Enums

ClassifyError

Error returned by classify_cpgs when the input violates the classifier’s preconditions: phased genotypes only, and no two variants whose REF spans overlap while both alt alleles land on a shared haplotype.

CpgPlacement

Where a single CpG (haplotype-coord pair) is recorded in the methylated VCF.

ReadError

Error returned by read_contig_methylation when the input VCF stream violates the writer’s encoding contract.

Constants

DEFAULT_METHYLATE_SAMPLE

Default sample column name used by methylate when no VCF sample is provided.

Functions

classify_cpgs

Classify every CpG on every haplotype into CpgPlacements.

load_contig_methylation_from_records

Look up the parsed methylation truth for a single contig from the pre-parsed MethylationVcfRecords.

parse_methylation_vcf

Read and split a methylation-annotated VCF into MethylationVcfRecords in a single pass: decompresses (BGZF or plain) once, detects whether the header declares MT/MB, and partitions data lines by contig.

read_contig_methylation

Parse MT/MB records from a per-contig VCF byte slice back into a crate::meth::ContigMethylation.

vcf_has_mt_mb_records

Check whether a VCF actually carries methylation truth: the header must declare both MT and MB FORMAT fields and at least one data record must list MT (or MB) in its FORMAT column.

write_contig

Write all methylation-only records for one contig as VCF text rows.

write_vcf_header

Write a VCF header for a methylation-annotated VCF to writer.