The MPHF maps each canonical kmer to an integer slot but provides no inverse: a slot index alone cannot reconstruct the kmer. The **evidence file** supplies this inverse: for each MPHF slot it stores a pointer into the unitig sequence file, from which k nucleotides can be extracted.
Unitigs are the natural compact representation: a run of L nucleotides encodes L − k + 1 consecutive canonical kmers. The entire kmer set of a partition is reconstructible from its unitig binary file.
Unitigs with more than `MAX_KMERS_PER_CHUNK = 256` k-mers are transparently split into overlapping chunks. Each chunk has at most 256 k-mers (= `seql − k + 1 ≤ 256`); consecutive chunks overlap by k−1 nucleotides so no kmer is lost:
One offset entry is stored every `2^block_bits` chunks; the array is sentinel-terminated (last entry = file size). `DEFAULT_BLOCK_BITS = 0` stores one offset per chunk (exact table, no scan).
File size = `n_slots × 4` bytes. `chunk_id` is the 0-based index of the record in `unitigs.bin`; `rank` is the position of the canonical kmer within that chunk (counting only canonical kmers). Encoding: `raw = (chunk_id << 7) | (rank & 0x7F)`. Decoding: `chunk_id = raw >> 7`, `rank = raw & 0x7F`.
Scans `unitigs.bin` sequentially: for each chunk at byte offset `offset`, if `chunk_count & mask == 0` (where `mask = (1 << block_bits) − 1`), appends `offset as u32` to `block_offsets`. After the scan, appends a sentinel (= total file size), then writes the `.idx` file. Called after the unitig file is fully written and closed.
-`open(path)` — smart default: if `unitigs.bin.idx` exists, delegates to `open_direct_access`; otherwise delegates to `open_sequential`. Prefer this in call sites that don't require one specific mode.
-`open_sequential(path)` — never reads `.idx`. Sequential iterators only; `chunk_start(i)` falls back to an O(i) mmap scan rather than panicking.
-`open_direct_access(path)` — requires `.idx` to be present. Enables O(1) or O(2^block_bits) `chunk_start(i)`, used by `verify_canonical_kmer` at query time.
`CanonicalKmerIter` — a clonable sequential iterator returned by `UnitigFileReader::iter_canonical_kmers()`. It holds an `Arc<Mmap>` so cloning resets the cursor to the start without reopening the file. This makes it usable with `par_bridge()` for parallel MPHF construction without random access.
When `.idx` is absent (`open_sequential`): `chunk_start(i)` performs an O(i) sequential mmap scan from offset 0. No panic — the function degrades gracefully. This degraded path is used by `find_strict()` on Approx layers (sequential scan of all canonical kmers).
Two memory accesses: one 4-byte read from `evidence.bin`, one packed-bit extraction from `unitigs.bin` via the mmap. The retrieved sequence is already canonical (only canonical kmers are inserted into the De Bruijn graph).
The rank field is 7 bits (max 127) even though chunks can contain up to 256 k-mers, because rank counts only canonical kmers within the chunk, and the canonical kmer count is at most half the total.
Strategy B (chunk_id + rank) is the implemented strategy. For *B. nana* (k=31, 256 partitions, P ≈ 10.4 M unique kmers/partition, U ≈ 275 k chunks/partition, m_u ≈ 37.9 kmers/chunk):
Comparison with strategy A (global nucleotide offset): `⌈log₂(P · (1 + (k−1)/m_u))⌉ = 25 bits`. Strategy A is theoretically 2 bits cheaper; strategy B's advantage is **locality** (decoding touches one chunk's cache lines) and a bounded, constant-width rank field independent of partition size.
The unitig extraction from `GraphDeBruijn` is **not deterministic**: two runs on identical input can produce different unitig counts and sequences while covering exactly the same canonical kmer set.
The hash map (`hashbrown::HashMap` with `Xxh3Builder`) has run-dependent iteration order. The `start_iter` first pass emits every node where `can_extend_left` is false — this includes true dead-ends and branch points (nodes with ≥2 left neighbours). When a branch point is encountered before its upstream neighbours, it claims the downstream chain and those upstream neighbours later produce length-k degenerate unitigs. When upstream neighbours appear first, they extend through the branch point.
Both cover the same 4 canonical kmers. Pure cycles are unaffected: all cycle nodes have both extensions present, so none are emitted in the first pass; each cycle produces exactly one unitig regardless of entry point (only the cut point varies).
Measured on *B. nana* (k=31, m=11), summing across all partitions:
| N partitions | m_u |
|---|---|
| 1 | 41.89 |
| 16 | 38.19 |
| 256 | 37.90 |
| 1 024 | 37.89 |
`m_u` is set by De Bruijn graph topology (heterozygosity, repeats, sequencing errors), not partition count. The variation from 1 to 1024 partitions is under 10%; within 16–1024 it is under 1%. Unitigs provide ~3.1× nucleotide compaction over super-kmers at 256 partitions.
Evidence cost decreases by 1 bit/kmer with each doubling of partition count (via `log₂ U = log₂(P/m_u)`). The sequence storage term `2 · (1 + (k−1)/m_u) ≈ 3.6 bits/kmer` is approximately constant.
`evidence.bin` can be replaced by `fingerprint.bin` at index build time (`--approx`) or after the fact (`reindex --approx`). The fingerprint stores b bits per MPHF slot (the low b bits of `kmer.seq_hash()`); verification becomes a single bitfield comparison instead of a unitig dereference. False-positive rate per k-mer query: 1/2^b. With the Findere z parameter, z consecutive k-mers must all match, reducing the effective window FP rate to 1/2^(b·z) while skipping z−1 of every z k-mers. No `.idx` file is written or read in approx mode.
See [Approximate evidence (Findere fingerprint)](evidence_elimination.md) for the full design and CLI parameters.
