# obilayeredmap crate - obikmer

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# obilayeredmap — layered kmer index crate

## Purpose

`obilayeredmap` implements a persistent, incrementally extensible kmer index. The index is organised in three levels: index root → partition → layer. Each layer covers a disjoint kmer set and wraps a `ptr_hash` MPHF with associated per-slot data. Adding a new dataset never rebuilds existing layers.

## Three usage modes

The MPHF + evidence infrastructure is the same for all modes. The payload varies.

Mode | Description | Payload type | Storage
--- | --- | --- | ---
1. Set | membership test only | `()` | —
2. Count | occurrences per kmer per sample | `PersistentCompactIntMatrix` | `counts/` directory
3. Presence/absence | which genomes contain each kmer | `PersistentBitMatrix` | `presence/` directory

Both `PersistentCompactIntMatrix` and `PersistentBitMatrix` come from the `obicompactvec` crate.

## MphfLayer — autonomous kmer → slot mapping

`MphfLayer` encapsulates the MPHF + evidence + unitig spine for one layer. It is independent of any payload data.

    pub struct MphfLayer {
        mphf:     Mphf,
        evidence: Evidence,
        unitigs:  UnitigFileReader,
        n:        usize,   // number of indexed kmers = number of MPHF slots
    }

Public API:

    impl MphfLayer {
        pub fn open(dir: &Path) -> OLMResult<Self>
        pub fn find(&self, kmer: CanonicalKmer) -> Option<usize>   // Some(slot) or None
        pub fn n(&self) -> usize
        pub fn unitig_writer(dir: &Path) -> OLMResult<UnitigFileWriter>
        pub(crate) fn build(
            dir: &Path,
            fill_slot: &mut impl FnMut(usize, CanonicalKmer) -> OLMResult<()>,
        ) -> OLMResult<usize>
    }

`find` returns `Some(slot)` only after verifying via evidence that the kmer is actually indexed. It returns `None` for absent keys (ptr_hash maps any input to a valid slot; evidence verification is the only correct-membership test).

`build` runs two sequential passes over `unitigs.bin`:

1. Pass 1: iterate all canonical kmers in parallel via rayon, construct and store `mphf.bin`. `new_from_par_iter` avoids materialising a full key `Vec`.
2. Pass 2: iterate again sequentially, fill `evidence.bin`, call `fill_slot(slot, kmer)` once per kmer for payload population. A compact `n/8`-byte seen-bitset verifies MPHF injectivity inline.

For empty layers (n = 0), `build` returns `Ok(0)` immediately after creating empty `mphf.bin` and `evidence.bin`.

## Layer\<D: LayerData> — MPHF + payload

`Layer<D>` pairs an `MphfLayer` with one payload store.

    pub trait LayerData: Sized {
        type Item;
        fn open(layer_dir: &Path) -> OLMResult<Self>;
        fn read(&self, slot: usize) -> Self::Item;
    }

    pub struct Layer<D: LayerData = ()> {
        mphf: MphfLayer,
        data: D,
    }

    pub struct Hit<T = ()> {
        pub slot: usize,
        pub data: T,
    }

`LayerData` covers the read path only (`open` + `read`). Build signatures differ between modes and are not in the trait.

Type | `Item` | Description
--- | --- | ---
`()` | `()` | mode 1 — membership only
`PersistentCompactIntMatrix` | `Box<[u32]>` | mode 2 — count matrix (one u32 per column per slot)
`PersistentBitMatrix` | `Box<[bool]>` | mode 3 — presence matrix (one bit per genome per slot)

Build signatures:

    // mode 1
    impl Layer<()> {
        pub fn build(out_dir: &Path) -> OLMResult<usize>
    }

    // mode 2
    impl Layer<PersistentCompactIntMatrix> {
        pub fn build(out_dir: &Path, count_of: impl Fn(CanonicalKmer) -> u32) -> OLMResult<usize>
        pub fn build_from_map(out_dir: &Path, counts: &HashMap<CanonicalKmer, u32>) -> OLMResult<usize>
    }

    // mode 3
    impl Layer<PersistentBitMatrix> {
        pub fn build_presence(
            out_dir: &Path,
            n_genomes: usize,
            present_in: impl Fn(CanonicalKmer, usize) -> bool,
        ) -> OLMResult<usize>
    }

All build impls delegate MPHF + evidence construction to `MphfLayer::build` via a mode-specific `fill_slot` callback. Mode 2 pre-reads `n_kmers` from `unitigs.bin` to size the `PersistentCompactIntMatrixBuilder` before calling `MphfLayer::build`. Mode 3 does the same for `PersistentBitMatrixBuilder`.

## LayeredStore\<S> and aggregation traits

`LayeredStore<S>` is a generic aggregation wrapper over `Vec<S>`. It propagates three traits from `obicompactvec::traits` up the hierarchy via blanket impls:

    pub struct LayeredStore<S>(pub Vec<S>);

    impl<S: ColumnWeights> ColumnWeights for LayeredStore<S> { … }  // Σ col_weights across inner stores
    impl<S: CountPartials> CountPartials  for LayeredStore<S> { … }  // element-wise Σ partials
    impl<S: BitPartials>   BitPartials    for LayeredStore<S> { … }  // element-wise Σ partials

Because blanket impls compose, `LayeredStore<LayeredStore<S>>` automatically inherits all three traits when `S` does — providing the partitioned level without a separate type.

Aggregation hierarchy:

    PersistentCompactIntMatrix                  implements CountPartials
    LayeredStore<PersistentCompactIntMatrix>         via blanket impl  (one partition)
    LayeredStore<LayeredStore<…>>                    via blanket impl  (partitioned index)

Leaf implementors (in `obicompactvec`):

Type | Traits
--- | ---
`PersistentCompactIntMatrix` | `ColumnWeights` (via `sum()`) + `CountPartials`
`PersistentBitMatrix` | `ColumnWeights` (via `count_ones()`) + `BitPartials`

`PersistentCompactIntVec` and `PersistentBitVec` do not implement these traits — they are single-column primitives, not matrix-level aggregators.

See Kmer index architecture for the full trait API and the two-pass normalised-metric pattern.

## On-disk structure

    index_root/                        ← LayeredMap (collection)
      meta.json
      part_00000/                      ← Partition
        layer_0/                       ← Layer
          mphf.bin           — ptr_hash MPHF (epserde format)
          unitigs.bin        — packed 2-bit nucleotide sequences
          unitigs.bin.idx    — UIDX index: n_unitigs, n_kmers, seqls[], packed_offsets[]
          evidence.bin       — n × u32, each = (chunk_id: 25 bits | rank: 7 bits), LE
          counts/            [mode 2] PersistentCompactIntMatrix
            meta.json          {"n": N, "n_cols": 1}
            col_000000.pciv
          presence/          [mode 3] PersistentBitMatrix
            meta.json          {"n": N, "n_cols": G}
            col_000000.pbiv
            …
        layer_1/
          …
      part_00001/
        …

Partition (`part_XXXXX/`): all kmers whose canonical minimiser hashes to this bucket. Partitions are independent and can be processed in parallel.

Layer (`layer_N/`): one `MphfLayer` plus optional payload. Layer 0 covers dataset A; layer 1 covers kmers in B absent from A; etc. Layers within a partition are always disjoint.

## Evidence encoding

`evidence.bin` is a flat `[u32; n]` array with no header. Each u32 encodes one slot:

    bits [31:7] = chunk_id (25 bits) — index of the unitig chunk
    bits [6:0]  = rank     (7 bits)  — kmer index within the chunk (0-based)

Decoding: `chunk_id = raw >> 7`, `rank = raw & 0x7F`. Reconstructing the kmer: read k nucleotides at position `rank` within unitig `chunk_id`.

For k=31, m=11, the observed maximum is ~46 kmers per chunk — well within the 127-kmer u7 capacity. The structural maximum from superkmer construction is k − m + 1 = 21 kmers/unitig; longer unitigs arise from paths spanning more than one superkmer.

## ptr_hash configuration

    type Mphf = PtrHash<
        u64,                              // key type: canonical kmer raw encoding
        CubicEps,                         // bucket fn: 2.4 bits/key, λ=3.5, α=0.99
        CachelineEfVec<Vec<CachelineEf>>, // remap: 11.6 bits/entry (Elias-Fano)
        Xx64,                             // hasher: XXH3-64 with seed
        Vec<u8>,                          // pilots
    >;

`Xx64` is chosen over `FxHash` because canonical kmer raw values are left-aligned u64 with structural zeros in the low bits (42 zeros for k=11, 2 zeros for k=31), which single-multiply hashes distribute poorly.

`CubicEps` with `PtrHashParams::<CubicEps>::default()` (λ=3.5) is a balanced tradeoff: 2× slower construction than `Linear/λ=3.0`, 20% less space.

## Query path

    pub fn query(&self, kmer: CanonicalKmer) -> Option<Hit<D::Item>> {
        self.mphf.find(kmer).map(|slot| Hit { slot, data: self.data.read(slot) })
    }

`MphfLayer::find` probes the MPHF, decodes evidence, and verifies the kmer — returning `Some(slot)` on match, `None` otherwise. `data.read(slot)` is called only on a confirmed hit.

In `LayeredMap`, layers are probed in order; the first match wins. Expected probe depth: 1 for kmers in layer 0.

## Add-layer algorithm

When adding dataset B to an existing index:

1. For each partition, probe existing layers for kmers of B routed to that partition.
2. Collect kmers absent from all layers → `B \ index`.
3. Write `B \ index` to a new `unitigs.bin` via `MphfLayer::unitig_writer`.
4. Call `Layer<D>::build` on the new directory.
5. Update `meta.json`.

Each partition's new layer is built independently; the operation is fully parallel across partitions.

## Dependencies

crate | role
--- | ---
`ptr_hash 1.1` | MPHF per layer
`cacheline-ef 1.1` | compact remap inside ptr_hash
`epserde 0.8` | zero-copy MPHF serialisation
`memmap2 0.9` | mmap of evidence and payload files
`obiskio` | unitig file writer/reader
`obicompactvec` | payload types + aggregation traits
`rayon 1` | parallel MPHF construction pass
`ndarray 0.16` | aggregation output arrays