Struct CpgTruthTally 

pub struct CpgTruthTally { /* private fields */ }

Per-(contig, top-C reference position) tally of methylated vs unmethylated calls. Indexed by (contig_index, ref_pos_of_top_C); the implied bedGraph end is ref_pos + 1 (matches MethylDackel).

Implementations

impl CpgTruthTally

pub fn new() -> Self

Empty tally.

pub fn record_mate( &mut self, contig_idx: usize, mate_ref_positions: &[u32], ref_cpgs: &[u32], methylation: &ContigMethylation, haplotype: &Haplotype, haplotype_index: usize, is_forward_fragment: bool, )

Record one mate’s contribution. mate_ref_positions is the per-base reference position list for the mate’s GENOMIC portion (no adapter), in ascending reference order. ref_cpgs is the precomputed sorted list of top-C reference CpG positions for this contig (caller pre- computes once per contig). is_forward_fragment distinguishes CT (top-strand-derived) from GA (bottom-strand-derived) fragments.

For CT fragments the call is read off top[hap_position_for(p)]; for GA fragments off bottom[hap_position_for(p+1)]. Both look up against the haplotype the fragment was sampled from. The bitmap is indexed by haplotype coordinates, so we map each reference CpG position through Haplotype::hap_position_for.

Panics

Panics if mate_ref_positions.last() is unreachable after the non-empty check (it cannot be — the early return covers that case).

pub fn write_bedgraph( &self, dict: &SequenceDictionary, path: &Path, ) -> Result<()>

Write the tally to path as a MethylDackel-format CpG bedGraph.

Format (tab-separated): chrom start end rate n_meth n_unmeth, preceded by a track header line. Sites are emitted in (contig index, reference position) order. rate is the integer percentage round(100 * n_meth / (n_meth + n_unmeth)). Sites with zero total coverage are skipped (they would not appear in MethylDackel’s output either).

Errors

Returns an error if the file cannot be created, if a contig index in the tally is missing from dict, or if any I/O write fails.

Trait Implementations

impl Debug for CpgTruthTally

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Default for CpgTruthTally

fn default() -> CpgTruthTally

Returns the “default value” for a type.