Function apply_methylation_conversion 

pub fn apply_methylation_conversion(
    bases: &mut [u8],
    n_genomic: usize,
    is_negative_strand: bool,
    hap_start: u32,
    haplotype_index: usize,
    config: &MethylationConfig<'_>,
    rng: &mut impl Rng,
) -> bool

Apply per-base methylation chemistry conversion to read bases in place.

bases are in read 5’->3’ orientation (FASTQ orientation). n_genomic is the number of leading bases that come from the haplotype (anything past n_genomic is adapter sequence and is left untouched). When is_negative_strand is true, bases[i] covers haplotype position hap_start + (n_genomic - 1 - i); otherwise hap_start + i.

haplotype_index selects which per-haplotype methylation table to use from the ContigMethylation in config.

Per-molecule conversion failure is drawn once here, before the per-base loop: with probability config.failure_rate the molecule is a failure and converts its should-convert cytosines at 1.0 - config.conversion_rate (near-zero), otherwise at config.conversion_rate. Because this runs once per fragment (via [crate::read::apply_fragment_chemistry]), both mates derive from the same converted buffer and stay coherent. Returns whether the molecule was drawn as a conversion failure so the caller can record it as ground truth.

Called between uppercase_in_place and apply_errors in crate::read::generate_read_pair’s build_mate helper. Chemistry runs before sequencing errors are applied (mirroring the biological order).

Panics

Panics if config.conversion_rate or config.failure_rate is not a finite value in [0.0, 1.0]. Mirrors the guard on MethylationTable::from_haplotype: the CLI validates this, but the function is pub, and an unguarded NaN / out-of-range rate would silently distort every chemistry draw.