Struct Haplotype 

pub struct Haplotype { /* private fields */ }

Sparse representation of one haplotype — a reference overlay of variants.

Instead of materializing a full haplotype sequence (which would require ~250MB per haplotype for human chr1), this stores only the differences from the reference as a sorted set of variants in a COITree for efficient range queries.

Fragment extraction works by walking the reference sequence and substituting alt alleles at variant positions on the fly.

Because coitrees requires Copy + Default for metadata, we store variant indices (as u32) in the tree and keep the actual variant data in a separate Vec.

Implementations

impl Haplotype

pub fn allele_index(&self) -> usize

Return the allele index of this haplotype.

pub fn extract_fragment( &self, reference: &[u8], ref_start: u32, fragment_len: usize, ) -> (Vec<u8>, Vec<u32>)

Extract a fragment from this haplotype at the given reference coordinates.

Walks the reference from ref_start and produces fragment_len bases, substituting alternate alleles where this haplotype has variants. Returns the fragment bases and a list of reference positions corresponding to each fragment base (for golden BAM coordinate mapping).

Arguments

• reference — Full reference sequence for this contig.
• ref_start — 0-based start position on the reference.
• fragment_len — Desired number of output bases.

Returns

A tuple of (fragment_bases, ref_positions) where ref_positions[i] is the reference position corresponding to fragment_bases[i]. For inserted bases, the reference position is that of the base preceding the insertion.