Struct ReferenceView 

pub struct ReferenceView<'a> { /* private fields */ }

A borrowed, zero-copy view over the persisted 2-bit forward reference (Reference2bit). Decodes bases on demand from the mmap — no full-reference allocation — so consumers (the aligner DP window in B4b, variants’ ref_base in B4c) read the reference from the .idx alone. Uses global (concatenated) coordinates; (contig, pos) mapping stays with ContigSet. The little-endian host requirement is the same as FmIndexView (checked in new).

Implementations

impl<'a> ReferenceView<'a>

pub fn len(&self) -> usize

Number of reference bases.

pub fn is_empty(&self) -> bool

Whether the reference is empty.

pub fn base_at(&self, global: usize) -> u8

The ASCII base at global position global. Mirrors CompressedDNA::base_at: a set ambiguity bit decodes to N, otherwise the 2-bit code maps to A/C/G/T.

pub fn decode_window(&self, start: usize, end: usize, out: &mut Vec<u8>)

Decode [start, end.min(len)) into out (cleared first). end is clamped to len, so an over-range request never panics; start <= end is the caller’s contract. Bounded by the window size — never the whole genome.

pub fn decode_window_arc(&self, start: usize, end: usize) -> Arc<[u8]>

Decode [start, end.min(len)) directly into an Arc<[u8]>, with no separate owned Vec materialized first. Arc::from(Vec<u8>) REALLOCATES — source and Arc buffers are both fully resident during the copy, so a per-contig decode briefly holds two copies of the contig (the reference- decode transient that broke the predicted-peak bound). Collecting a TrustedLen range straight into the Arc writes into its allocation in place, so peak resident reference memory is ONE copy. Byte-identical to decode_window; bounded by the window size.

Trait Implementations

impl<'a> Debug for ReferenceView<'a>

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

Formats the value using the given formatter.