src/obikindex/src/layer/content_layer.rs

@@ -28,9 +28,11 @@ use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
 use obikseq::CanonicalKmer;
 
 use crate::layer::error::OLMResult;
-use crate::layer::typed_layer::{LayerContent, TypedLayer, COUNTS_DIR, PRESENCE_DIR};
 use crate::layer::meta::IndexMode;
-use crate::layer::mphf_layer::{EvidenceKind, EVIDENCE_FILE, FINGERPRINT_FILE, MPHF_FILE, UNITIGS_FILE};
+use crate::layer::mphf_layer::{
+    EVIDENCE_FILE, EvidenceKind, FINGERPRINT_FILE, MPHF_FILE, UNITIGS_FILE,
+};
+use crate::layer::typed_layer::{COUNTS_DIR, LayerContent, PRESENCE_DIR, TypedLayer};
 
 /// One layer, at any point in its life — see the module docs. Only
 /// [`Empty`](Layer::Empty) and the two ready-to-read states
@@ -42,7 +44,9 @@ pub enum Layer {
     /// the path accessors panics on this variant: calling them means the
     /// caller assumed a layer was ready when it wasn't, an implementation
     /// error to surface loudly, not paper over with a default value.
-    Empty { dir: PathBuf },
+    Empty {
+        dir: PathBuf,
+    },
     Count(TypedLayer<PersistentCompactIntMatrix>),
     Presence(TypedLayer<PersistentBitMatrix>),
 }
@@ -53,7 +57,9 @@ impl Layer {
     /// building a new layer.
     pub fn create(dir: &Path) -> std::io::Result<Self> {
         std::fs::create_dir_all(dir)?;
-        Ok(Layer::Empty { dir: dir.to_owned() })
+        Ok(Layer::Empty {
+            dir: dir.to_owned(),
+        })
     }
 
     /// Open one layer, auto-detecting count vs. presence from what is
@@ -66,7 +72,8 @@ impl Layer {
     /// here.
     pub fn open(layer_dir: &Path, mode: &IndexMode, with_counts: bool) -> OLMResult<Self> {
         if with_counts && layer_dir.join(COUNTS_DIR).exists() {
-            return TypedLayer::<PersistentCompactIntMatrix>::open(layer_dir, mode).map(Layer::Count);
+            return TypedLayer::<PersistentCompactIntMatrix>::open(layer_dir, mode)
+                .map(Layer::Count);
         }
         TypedLayer::<PersistentBitMatrix>::open(layer_dir, mode).map(Layer::Presence)
     }
@@ -91,12 +98,24 @@ impl Layer {
         }
     }
 
-    pub fn mphf_path(&self) -> PathBuf { self.dir().join(MPHF_FILE) }
-    pub fn unitigs_path(&self) -> PathBuf { self.dir().join(UNITIGS_FILE) }
-    pub fn evidence_path(&self) -> PathBuf { self.dir().join(EVIDENCE_FILE) }
-    pub fn fingerprint_path(&self) -> PathBuf { self.dir().join(FINGERPRINT_FILE) }
-    pub fn counts_dir(&self) -> PathBuf { self.dir().join(COUNTS_DIR) }
-    pub fn presence_dir(&self) -> PathBuf { self.dir().join(PRESENCE_DIR) }
+    pub fn mphf_path(&self) -> PathBuf {
+        self.dir().join(MPHF_FILE)
+    }
+    pub fn unitigs_path(&self) -> PathBuf {
+        self.dir().join(UNITIGS_FILE)
+    }
+    pub fn evidence_path(&self) -> PathBuf {
+        self.dir().join(EVIDENCE_FILE)
+    }
+    pub fn fingerprint_path(&self) -> PathBuf {
+        self.dir().join(FINGERPRINT_FILE)
+    }
+    pub fn counts_dir(&self) -> PathBuf {
+        self.dir().join(COUNTS_DIR)
+    }
+    pub fn presence_dir(&self) -> PathBuf {
+        self.dir().join(PRESENCE_DIR)
+    }
 
     // ── Ready-only surface ───────────────────────────────────────────────
 
@@ -135,11 +154,11 @@ impl Layer {
     /// Raw MPHF batch lookup: kmer → slot, no membership check — for
     /// callers that already know every kmer is a member of *this* layer, so
     /// the evidence check `find_slot`/`find` would perform is redundant.
-    pub fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+    pub fn hash_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
         match self {
-            Layer::Count(l) => l.index_batch(kmers),
-            Layer::Presence(l) => l.index_batch(kmers),
-            Layer::Empty { .. } => panic!("Layer::index_batch() called on an Empty layer"),
+            Layer::Count(l) => l.hash_batch(kmers),
+            Layer::Presence(l) => l.hash_batch(kmers),
+            Layer::Empty { .. } => panic!("Layer::hash_batch() called on an Empty layer"),
         }
     }
 
@@ -168,7 +187,61 @@ impl Layer {
                     o.extend(c.iter().map(|&v| v != 0));
                 }
             }
-            Layer::Empty { .. } => panic!("Layer::fill_sub_matrix_carries() called on an Empty layer"),
+            Layer::Empty { .. } => {
+                panic!("Layer::fill_sub_matrix_carries() called on an Empty layer")
+            }
+        }
+    }
+
+    /// Raw MPHF lookup: kmer → slot, no membership check.
+    pub fn hash(&self, kmer: CanonicalKmer) -> usize {
+        match self {
+            Layer::Count(l) => l.hash(kmer),
+            Layer::Presence(l) => l.hash(kmer),
+            Layer::Empty { .. } => panic!("Layer::hash() called on an Empty layer"),
+        }
+    }
+
+    /// Iterate over all canonical kmers in the layer, in deterministic order.
+    pub fn iter_kmers(&self) -> crate::layer::mphf_layer::KmerIter {
+        match self {
+            Layer::Count(l) => l.iter_kmers(),
+            Layer::Presence(l) => l.iter_kmers(),
+            Layer::Empty { .. } => panic!("Layer::iter_kmers() called on an Empty layer"),
+        }
+    }
+
+    /// Iterate over all canonical kmers, each paired with its zero-based
+    /// sequence index in `unitigs.bin`.
+    pub fn enumerate_kmers(&self) -> std::iter::Enumerate<crate::layer::mphf_layer::KmerIter> {
+        match self {
+            Layer::Count(l) => l.enumerate_kmers(),
+            Layer::Presence(l) => l.enumerate_kmers(),
+            Layer::Empty { .. } => panic!("Layer::enumerate_kmers() called on an Empty layer"),
+        }
+    }
+
+    /// Iterate over the layer's canonical kmers in batches of `n`.
+    pub fn iter_kmers_batch(&self, n: usize) -> crate::layer::mphf_layer::KmerBatchIter {
+        match self {
+            Layer::Count(l) => l.iter_kmers_batch(n),
+            Layer::Presence(l) => l.iter_kmers_batch(n),
+            Layer::Empty { .. } => panic!("Layer::iter_kmers_batch() called on an Empty layer"),
+        }
+    }
+
+    /// Iterate over batches, each paired with the zero-based index of the
+    /// first kmer in the batch.
+    pub fn enumerate_kmers_batch(
+        &self,
+        n: usize,
+    ) -> Box<dyn Iterator<Item = (usize, Vec<CanonicalKmer>)> + Send + 'static> {
+        match self {
+            Layer::Count(l) => Box::new(l.enumerate_kmers_batch(n)),
+            Layer::Presence(l) => Box::new(l.enumerate_kmers_batch(n)),
+            Layer::Empty { .. } => {
+                panic!("Layer::enumerate_kmers_batch() called on an Empty layer")
+            }
         }
     }
 }

src/obikindex/src/layer/mphf_layer.rs

@@ -15,9 +15,9 @@ use crate::layer::evidence::{Evidence, EvidenceWriter};
 use crate::layer::fingerprint::{FingerprintVec, FingerprintVecWriter};
 use crate::layer::meta::IndexMode;
 
-pub(crate) const MPHF_FILE:        &str = "mphf.bin";
-pub(crate) const UNITIGS_FILE:     &str = "unitigs.bin";
-pub(crate) const EVIDENCE_FILE:    &str = "evidence.bin";
+pub(crate) const MPHF_FILE: &str = "mphf.bin";
+pub(crate) const UNITIGS_FILE: &str = "unitigs.bin";
+pub(crate) const EVIDENCE_FILE: &str = "evidence.bin";
 pub(crate) const FINGERPRINT_FILE: &str = "fingerprint.bin";
 
 /// Owned MPHF — used only at build time (construction + store).
@@ -30,9 +30,20 @@ type MphfEps = PtrHash<u64, CubicEps, CachelineEfVec<&'static [CachelineEf]>, Xx
 // ── LayerEvidence ─────────────────────────────────────────────────────────────
 
 enum LayerEvidence {
-    Exact  { evidence: Evidence, unitigs: Arc<UnitigFileReader> },
-    Approx { fingerprint: FingerprintVec, unitigs: Arc<UnitigFileReader>, unitigs_path: PathBuf },
-    Hybrid { evidence: Evidence, unitigs: Arc<UnitigFileReader>, fingerprint: FingerprintVec },
+    Exact {
+        evidence: Evidence,
+        unitigs: Arc<UnitigFileReader>,
+    },
+    Approx {
+        fingerprint: FingerprintVec,
+        unitigs: Arc<UnitigFileReader>,
+        unitigs_path: PathBuf,
+    },
+    Hybrid {
+        evidence: Evidence,
+        unitigs: Arc<UnitigFileReader>,
+        fingerprint: FingerprintVec,
+    },
 }
 
 // ── EvidenceKind ──────────────────────────────────────────────────────────────
@@ -51,14 +62,15 @@ impl EvidenceKind {
     /// `evidence.bin`/`fingerprint.bin` alone determines the mode — same
     /// signal `MphfLayer::open` uses, just without opening either file.
     pub fn detect(layer_dir: &Path) -> OLMResult<EvidenceKind> {
-        let has_evidence    = layer_dir.join(EVIDENCE_FILE).exists();
+        let has_evidence = layer_dir.join(EVIDENCE_FILE).exists();
         let has_fingerprint = layer_dir.join(FINGERPRINT_FILE).exists();
         match (has_evidence, has_fingerprint) {
-            (true, false)  => Ok(EvidenceKind::Exact),
-            (false, true)  => Ok(EvidenceKind::Approx),
-            (true, true)   => Ok(EvidenceKind::Hybrid),
+            (true, false) => Ok(EvidenceKind::Exact),
+            (false, true) => Ok(EvidenceKind::Approx),
+            (true, true) => Ok(EvidenceKind::Hybrid),
             (false, false) => Err(OLMError::InvalidLayer(format!(
-                "no evidence.bin or fingerprint.bin in {}", layer_dir.display()
+                "no evidence.bin or fingerprint.bin in {}",
+                layer_dir.display()
             ))),
         }
     }
@@ -74,8 +86,8 @@ impl EvidenceKind {
 ///   O(n) sequential scan on Approx layers.
 pub struct MphfLayer {
     mphf: MemCase<MphfEps>,
-    ev:   LayerEvidence,
-    n:    usize,
+    ev: LayerEvidence,
+    n: usize,
 }
 
 impl MphfLayer {
@@ -96,14 +108,28 @@ impl MphfLayer {
                 let n = fingerprint.n();
                 let unitigs = Arc::new(UnitigFileReader::open(&dir.join(UNITIGS_FILE))?);
                 let unitigs_path = dir.join(UNITIGS_FILE);
-                (LayerEvidence::Approx { fingerprint, unitigs, unitigs_path }, n)
+                (
+                    LayerEvidence::Approx {
+                        fingerprint,
+                        unitigs,
+                        unitigs_path,
+                    },
+                    n,
+                )
             }
             IndexMode::Hybrid { .. } => {
-                let evidence    = Evidence::open(&dir.join(EVIDENCE_FILE))?;
+                let evidence = Evidence::open(&dir.join(EVIDENCE_FILE))?;
                 let fingerprint = FingerprintVec::open(&dir.join(FINGERPRINT_FILE))?;
                 let n = evidence.len();
                 let unitigs = Arc::new(UnitigFileReader::open(&dir.join(UNITIGS_FILE))?);
-                (LayerEvidence::Hybrid { evidence, unitigs, fingerprint }, n)
+                (
+                    LayerEvidence::Hybrid {
+                        evidence,
+                        unitigs,
+                        fingerprint,
+                    },
+                    n,
+                )
             }
         };
         Ok(Self { mphf, ev, n })
@@ -118,9 +144,13 @@ impl MphfLayer {
     #[inline]
     pub fn find(&self, kmer: CanonicalKmer) -> Option<usize> {
         let slot = self.mphf.index(&kmer.raw());
-        if slot >= self.n { return None; }
+        if slot >= self.n {
+            return None;
+        }
         match &self.ev {
-            LayerEvidence::Exact { evidence, unitigs, .. } => {
+            LayerEvidence::Exact {
+                evidence, unitigs, ..
+            } => {
                 let (chunk_id, rank) = evidence.decode(slot);
                 if unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
                     Some(slot)
@@ -128,9 +158,13 @@ impl MphfLayer {
                     None
                 }
             }
-            LayerEvidence::Approx { fingerprint, .. } |
-            LayerEvidence::Hybrid { fingerprint, .. } => {
-                if fingerprint.matches(slot, kmer.seq_hash()) { Some(slot) } else { None }
+            LayerEvidence::Approx { fingerprint, .. }
+            | LayerEvidence::Hybrid { fingerprint, .. } => {
+                if fingerprint.matches(slot, kmer.seq_hash()) {
+                    Some(slot)
+                } else {
+                    None
+                }
             }
         }
     }
@@ -142,10 +176,16 @@ impl MphfLayer {
     ///   that owns the slot, then exact comparison.
     pub fn find_strict(&self, kmer: CanonicalKmer) -> Option<usize> {
         let slot = self.mphf.index(&kmer.raw());
-        if slot >= self.n { return None; }
+        if slot >= self.n {
+            return None;
+        }
         match &self.ev {
-            LayerEvidence::Exact  { evidence, unitigs, .. } |
-            LayerEvidence::Hybrid { evidence, unitigs, .. } => {
+            LayerEvidence::Exact {
+                evidence, unitigs, ..
+            }
+            | LayerEvidence::Hybrid {
+                evidence, unitigs, ..
+            } => {
                 let (chunk_id, rank) = evidence.decode(slot);
                 if unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
                     Some(slot)
@@ -165,38 +205,16 @@ impl MphfLayer {
         }
     }
 
-    /// Reconstruct the canonical k-mer stored at `slot` — the inverse of
-    /// [`find`](Self::find)/[`find_strict`](Self::find_strict) (k-mer → slot).
-    /// O(1) on `Exact`/`Hybrid` layers: `evidence.decode(slot)` gives
-    /// `(chunk_id, rank)` directly (no MPHF hashing, no file scan), then
-    /// `unitigs.canonical_raw_kmer` is a direct-access read. `None` on
-    /// `Approx` layers — fingerprints alone can't recover a k-mer, and
-    /// falling back to a full sequential scan here would silently make one
-    /// call cost O(n); callers needing this on an `Approx` layer should
-    /// scan `unitigs.bin` themselves and decide how to handle that cost
-    /// explicitly.
-    pub fn kmer_at(&self, slot: usize) -> Option<CanonicalKmer> {
-        if slot >= self.n {
-            return None;
-        }
-        match &self.ev {
-            LayerEvidence::Exact  { evidence, unitigs, .. } |
-            LayerEvidence::Hybrid { evidence, unitigs, .. } => {
-                let (chunk_id, rank) = evidence.decode(slot);
-                let raw = unitigs.canonical_raw_kmer(chunk_id as usize, rank as usize);
-                Some(CanonicalKmer::from_raw_unchecked(raw))
-            }
-            LayerEvidence::Approx { .. } => None,
-        }
+    /// Number of slots in the MPHF layer — equal to the number of stored k-mers.
+    pub fn n(&self) -> usize {
+        self.n
     }
 
-    pub fn n(&self) -> usize { self.n }
-
     /// This already-open layer's evidence mode — reads the discriminant
     /// already in memory, no disk access.
     pub fn evidence_kind(&self) -> EvidenceKind {
         match &self.ev {
-            LayerEvidence::Exact  { .. } => EvidenceKind::Exact,
+            LayerEvidence::Exact { .. } => EvidenceKind::Exact,
             LayerEvidence::Approx { .. } => EvidenceKind::Approx,
             LayerEvidence::Hybrid { .. } => EvidenceKind::Hybrid,
         }
@@ -208,7 +226,7 @@ impl MphfLayer {
     /// check against the layer's evidence.  The returned slot is only meaningful
     /// when the kmer is actually present in the layer; callers that need an
     /// existence test should use [`find`](Self::find) instead.
-    pub fn index(&self, kmer: CanonicalKmer) -> usize {
+    pub fn hash(&self, kmer: CanonicalKmer) -> usize {
         self.mphf.index(&kmer.raw())
     }
 
@@ -217,7 +235,7 @@ impl MphfLayer {
     /// Returns a [`Vec`] of slots, one per input kmer, in the same order as the
     /// input slice.  Like [`index`](Self::index), no membership check is
     /// performed.
-    pub fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+    pub fn hash_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
         kmers.iter().map(|k| self.mphf.index(&k.raw())).collect()
     }
 
@@ -237,7 +255,9 @@ impl MphfLayer {
             LayerEvidence::Approx { unitigs, .. } => unitigs,
             LayerEvidence::Hybrid { unitigs, .. } => unitigs,
         };
-        KmerIter { inner: Box::new(reader.iter_indexed_canonical_kmers_owned()) }
+        KmerIter {
+            inner: Box::new(reader.iter_indexed_canonical_kmers_owned()),
+        }
     }
 
     /// Iterate over all canonical kmers, each paired with its zero-based
@@ -255,7 +275,10 @@ impl MphfLayer {
     /// Each call to [`next`](Iterator::next) returns a [`Vec`] of up to `n`
     /// kmers.  The final batch may be shorter when the layer is exhausted.
     pub fn iter_kmers_batch(&self, n: usize) -> KmerBatchIter {
-        KmerBatchIter { inner: self.iter_kmers(), batch_size: n }
+        KmerBatchIter {
+            inner: self.iter_kmers(),
+            batch_size: n,
+        }
     }
 
     /// Iterate over batches, each paired with the zero-based index of the
@@ -265,7 +288,10 @@ impl MphfLayer {
     /// `batch_start_index` is the iteration-order offset of the first kmer
     /// in that batch within the full layer sequence — i.e. a multiple of `n`
     /// except for the final (possibly shorter) batch.
-    pub fn enumerate_kmers_batch(&self, n: usize) -> impl Iterator<Item = (usize, Vec<CanonicalKmer>)> + Send + 'static {
+    pub fn enumerate_kmers_batch(
+        &self,
+        n: usize,
+    ) -> impl Iterator<Item = (usize, Vec<CanonicalKmer>)> + Send + 'static {
         let mut offset = 0usize;
         self.iter_kmers_batch(n).map(move |batch| {
             let base = offset;
@@ -320,11 +346,7 @@ impl Iterator for KmerBatchIter {
                 break;
             }
         }
-        if batch.is_empty() {
-            None
-        } else {
-            Some(batch)
-        }
+        if batch.is_empty() { None } else { Some(batch) }
     }
 }
 
@@ -373,7 +395,7 @@ impl MphfLayer {
         let mphf: Mphf = Mphf::load_full(&dir.join(MPHF_FILE))
             .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
 
-        let mut ev   = EvidenceWriter::new(n);
+        let mut ev = EvidenceWriter::new(n);
         let mut seen = vec![0u8; (n + 7) / 8];
 
         for (kmer, chunk_id, rank) in unitigs.iter_indexed_canonical_kmers() {
@@ -382,7 +404,7 @@ impl MphfLayer {
                 return Err(OLMError::Mphf("slot out of bounds".into()));
             }
             let byte = slot / 8;
-            let bit  = 1u8 << (slot % 8);
+            let bit = 1u8 << (slot % 8);
             if seen[byte] & bit != 0 {
                 return Err(OLMError::Mphf("duplicate slot".into()));
             }
@@ -398,7 +420,9 @@ impl MphfLayer {
     /// Build `fingerprint.bin` from `unitigs.bin` + `mphf.bin`.
     pub fn build_approx_evidence(dir: &Path, b: u8, z: u8) -> OLMResult<usize> {
         if b == 0 || b > 64 {
-            return Err(OLMError::InvalidLayer("fingerprint width must be 1..=64".into()));
+            return Err(OLMError::InvalidLayer(
+                "fingerprint width must be 1..=64".into(),
+            ));
         }
         if z == 0 {
             return Err(OLMError::InvalidLayer("z must be ≥ 1".into()));
@@ -452,9 +476,8 @@ impl MphfLayer {
 
         // ── Empty layer ───────────────────────────────────────────────────────
         if n == 0 {
-            let mphf: Mphf =
-                Mphf::try_new(&[] as &[u64], PtrHashParams::<CubicEps>::default())
-                    .ok_or_else(|| OLMError::Mphf("construction failed".into()))?;
+            let mphf: Mphf = Mphf::try_new(&[] as &[u64], PtrHashParams::<CubicEps>::default())
+                .ok_or_else(|| OLMError::Mphf("construction failed".into()))?;
             mphf.store(&dir.join(MPHF_FILE))
                 .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
             match mode {
@@ -474,9 +497,11 @@ impl MphfLayer {
 
         // ── Pass 1: MPHF via clonable mmap iterator ───────────────────────────
         let keys = CanonicalKmerIter::new(&unitig_path).map_err(sk_to_olm)?;
-        let mphf: Mphf =
-            Mphf::new_from_par_iter(n, keys.map(|k| k.raw()).par_bridge(),
-                                    PtrHashParams::<CubicEps>::default());
+        let mphf: Mphf = Mphf::new_from_par_iter(
+            n,
+            keys.map(|k| k.raw()).par_bridge(),
+            PtrHashParams::<CubicEps>::default(),
+        );
         mphf.store(&dir.join(MPHF_FILE))
             .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
 
@@ -489,9 +514,14 @@ impl MphfLayer {
                 let mut ev = EvidenceWriter::new(n);
                 for (kmer, chunk_id, rank) in unitigs2.iter_indexed_canonical_kmers() {
                     let slot = mphf.index(&kmer.raw());
-                    if slot >= n { return Err(OLMError::Mphf("slot out of bounds".into())); }
-                    let byte = slot / 8; let bit = 1u8 << (slot % 8);
-                    if seen[byte] & bit != 0 { return Err(OLMError::Mphf("duplicate slot".into())); }
+                    if slot >= n {
+                        return Err(OLMError::Mphf("slot out of bounds".into()));
+                    }
+                    let byte = slot / 8;
+                    let bit = 1u8 << (slot % 8);
+                    if seen[byte] & bit != 0 {
+                        return Err(OLMError::Mphf("duplicate slot".into()));
+                    }
                     seen[byte] |= bit;
                     ev.set(slot, chunk_id as u32, rank as u8);
                     fill_slot(slot, kmer)?;
@@ -504,9 +534,14 @@ impl MphfLayer {
                 let mut fw = FingerprintVecWriter::new(n, *b);
                 for (kmer, _, _) in unitigs2.iter_indexed_canonical_kmers() {
                     let slot = mphf.index(&kmer.raw());
-                    if slot >= n { return Err(OLMError::Mphf("slot out of bounds".into())); }
-                    let byte = slot / 8; let bit = 1u8 << (slot % 8);
-                    if seen[byte] & bit != 0 { return Err(OLMError::Mphf("duplicate slot".into())); }
+                    if slot >= n {
+                        return Err(OLMError::Mphf("slot out of bounds".into()));
+                    }
+                    let byte = slot / 8;
+                    let bit = 1u8 << (slot % 8);
+                    if seen[byte] & bit != 0 {
+                        return Err(OLMError::Mphf("duplicate slot".into()));
+                    }
                     seen[byte] |= bit;
                     fw.set(slot, kmer.seq_hash());
                     fill_slot(slot, kmer)?;
@@ -519,9 +554,14 @@ impl MphfLayer {
                 let mut fw = FingerprintVecWriter::new(n, *b);
                 for (kmer, chunk_id, rank) in unitigs2.iter_indexed_canonical_kmers() {
                     let slot = mphf.index(&kmer.raw());
-                    if slot >= n { return Err(OLMError::Mphf("slot out of bounds".into())); }
-                    let byte = slot / 8; let bit = 1u8 << (slot % 8);
-                    if seen[byte] & bit != 0 { return Err(OLMError::Mphf("duplicate slot".into())); }
+                    if slot >= n {
+                        return Err(OLMError::Mphf("slot out of bounds".into()));
+                    }
+                    let byte = slot / 8;
+                    let bit = 1u8 << (slot % 8);
+                    if seen[byte] & bit != 0 {
+                        return Err(OLMError::Mphf("duplicate slot".into()));
+                    }
                     seen[byte] |= bit;
                     ev.set(slot, chunk_id as u32, rank as u8);
                     fw.set(slot, kmer.seq_hash());

src/obikindex/src/layer/typed_layer.rs

@@ -3,10 +3,8 @@ use std::fs;
 use std::path::{Path, PathBuf};
 
 use obicompactvec::{
-    BinaryMatrix,
-    PersistentBitMatrix, PersistentBitMatrixBuilder,
-    PersistentCompactIntMatrix, PersistentCompactIntMatrixBuilder,
-    PersistentSparseBitMatrix,
+    BinaryMatrix, PersistentBitMatrix, PersistentBitMatrixBuilder, PersistentCompactIntMatrix,
+    PersistentCompactIntMatrixBuilder, PersistentSparseBitMatrix,
 };
 use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileReader, UnitigFileWriter};
@@ -16,7 +14,7 @@ use crate::layer::meta::IndexMode;
 use crate::layer::mphf_layer::MphfLayer;
 pub(crate) use crate::layer::mphf_layer::UNITIGS_FILE;
 
-pub(crate) const COUNTS_DIR:   &str = "counts";
+pub(crate) const COUNTS_DIR: &str = "counts";
 pub(crate) const PRESENCE_DIR: &str = "presence";
 
 // ── Trait ─────────────────────────────────────────────────────────────────────
@@ -82,7 +80,9 @@ pub fn open_data<D: LayerData>(root: &Path, i: usize) -> OLMResult<D> {
 
 impl LayerData for () {
     type Item = ();
-    fn open(_layer_dir: &Path) -> OLMResult<Self> { Ok(()) }
+    fn open(_layer_dir: &Path) -> OLMResult<Self> {
+        Ok(())
+    }
     fn read(&self, _slot: usize) {}
 }
 
@@ -91,7 +91,9 @@ impl LayerData for PersistentCompactIntMatrix {
     fn open(layer_dir: &Path) -> OLMResult<Self> {
         PersistentCompactIntMatrix::open(layer_dir).map_err(OLMError::Io)
     }
-    fn read(&self, slot: usize) -> Box<[u32]> { self.row(slot) }
+    fn read(&self, slot: usize) -> Box<[u32]> {
+        self.row(slot)
+    }
 }
 
 impl LayerData for PersistentBitMatrix {
@@ -99,7 +101,9 @@ impl LayerData for PersistentBitMatrix {
     fn open(layer_dir: &Path) -> OLMResult<Self> {
         PersistentBitMatrix::open(layer_dir).map_err(OLMError::Io)
     }
-    fn read(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
+    fn read(&self, slot: usize) -> Box<[bool]> {
+        self.row(slot)
+    }
 }
 
 impl LayerData for PersistentSparseBitMatrix {
@@ -107,7 +111,9 @@ impl LayerData for PersistentSparseBitMatrix {
     fn open(layer_dir: &Path) -> OLMResult<Self> {
         PersistentSparseBitMatrix::open(&layer_dir.join(PRESENCE_DIR)).map_err(OLMError::Io)
     }
-    fn read(&self, slot: usize) -> Box<[bool]> { self.row(slot) }
+    fn read(&self, slot: usize) -> Box<[bool]> {
+        self.row(slot)
+    }
 }
 
 // ── LayerContent ─────────────────────────────────────────────────────────────
@@ -202,7 +208,10 @@ impl<D: LayerData> TypedLayer<D> {
     }
 
     pub fn query(&self, kmer: CanonicalKmer) -> Option<Hit<D::Item>> {
-        self.mphf.find(kmer).map(|slot| Hit { slot, data: self.data.read(slot) })
+        self.mphf.find(kmer).map(|slot| Hit {
+            slot,
+            data: self.data.read(slot),
+        })
     }
 
     /// MPHF + evidence membership check only — no data read. For callers
@@ -214,16 +223,18 @@ impl<D: LayerData> TypedLayer<D> {
         self.mphf.find(kmer)
     }
 
-    pub fn n(&self) -> usize { self.mphf.n() }
+    pub fn n(&self) -> usize {
+        self.mphf.n()
+    }
 
     /// Raw MPHF lookup: kmer → slot, no membership check.
-    pub fn index(&self, kmer: CanonicalKmer) -> usize {
-        self.mphf.index(kmer)
+    pub fn hash(&self, kmer: CanonicalKmer) -> usize {
+        self.mphf.hash(kmer)
     }
 
     /// Batch raw MPHF lookup: kmers → slots, no membership check.
-    pub fn index_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
-        self.mphf.index_batch(kmers)
+    pub fn hash_batch(&self, kmers: &[CanonicalKmer]) -> Vec<usize> {
+        self.mphf.hash_batch(kmers)
     }
 
     /// Iterate over all canonical kmers in the layer, in deterministic order.
@@ -244,7 +255,10 @@ impl<D: LayerData> TypedLayer<D> {
 
     /// Iterate over batches, each paired with the zero-based index of the
     /// first kmer in the batch.
-    pub fn enumerate_kmers_batch(&self, n: usize) -> impl Iterator<Item = (usize, Vec<CanonicalKmer>)> + Send + 'static {
+    pub fn enumerate_kmers_batch(
+        &self,
+        n: usize,
+    ) -> impl Iterator<Item = (usize, Vec<CanonicalKmer>)> + Send + 'static {
         self.mphf.enumerate_kmers_batch(n)
     }
 
@@ -301,8 +315,12 @@ impl TypedLayer<()> {
     pub fn init_presence_matrix(layer_dir: &Path, n_kmers: usize) -> OLMResult<()> {
         let presence_dir = layer_dir.join(PRESENCE_DIR);
         fs::create_dir_all(&presence_dir).map_err(OLMError::Io)?;
-        let mut mb = PersistentBitMatrixBuilder::new(n_kmers, &presence_dir).map_err(OLMError::Io)?;
-        mb.add_col_ones().map_err(OLMError::Io)?.close().map_err(OLMError::Io)?;
+        let mut mb =
+            PersistentBitMatrixBuilder::new(n_kmers, &presence_dir).map_err(OLMError::Io)?;
+        mb.add_col_ones()
+            .map_err(OLMError::Io)?
+            .close()
+            .map_err(OLMError::Io)?;
         mb.close().map_err(OLMError::Io)
     }
 }
@@ -318,8 +336,8 @@ impl TypedLayer<PersistentCompactIntMatrix> {
     ) -> OLMResult<usize> {
         let n = UnitigFileReader::open_sequential(&out_dir.join(UNITIGS_FILE))?.n_kmers();
         let counts_dir = out_dir.join(COUNTS_DIR);
-        let mut mb = PersistentCompactIntMatrixBuilder::new(n, &counts_dir)
-            .map_err(OLMError::Io)?;
+        let mut mb =
+            PersistentCompactIntMatrixBuilder::new(n, &counts_dir).map_err(OLMError::Io)?;
         let mut col = mb.add_col().map_err(OLMError::Io)?;
         let n_built = MphfLayer::build(out_dir, block_bits, mode, &mut |slot, kmer| {
             col.set(slot, count_of(kmer));
@@ -336,7 +354,9 @@ impl TypedLayer<PersistentCompactIntMatrix> {
         mode: &IndexMode,
         counts: &HashMap<CanonicalKmer, u32>,
     ) -> OLMResult<usize> {
-        Self::build(out_dir, block_bits, mode, |kmer| counts.get(&kmer).copied().unwrap_or(0))
+        Self::build(out_dir, block_bits, mode, |kmer| {
+            counts.get(&kmer).copied().unwrap_or(0)
+        })
     }
 }
 

src/obikphylo/src/siblings/cache.rs

@@ -1,7 +1,7 @@
 use rayon::prelude::*;
 
-use obikseq::CanonicalKmer;
 use obikindex::layer::Layer;
+use obikseq::CanonicalKmer;
 use obisys::progress_bar;
 
 use obikindex::{KmerIndex, OKIResult};
@@ -45,11 +45,7 @@ pub(super) struct PartitionCache {
 }
 
 impl PartitionCache {
-    pub(super) fn build(
-        index: &KmerIndex,
-        n_parts: usize,
-        with_counts: bool,
-    ) -> OKIResult<Self> {
+    pub(super) fn build(index: &KmerIndex, n_parts: usize, with_counts: bool) -> OKIResult<Self> {
         let pb = progress_bar("open_partitions", n_parts as u64, "partitions");
         let built: Vec<(Vec<Layer>, usize)> = (0..n_parts)
             .into_par_iter()
@@ -200,7 +196,7 @@ impl PartitionCache {
             let mat = &mats[li];
             let variants: Vec<CanonicalKmer> =
                 entries.iter().map(|&(variant, _, _)| variant).collect();
-            let slots = mat.index_batch(&variants);
+            let slots = mat.hash_batch(&variants);
             let hits: Vec<(usize, usize, u8)> = slots
                 .into_iter()
                 .zip(entries.iter())

src/obikphylo/src/siblings/family_scan.rs

@@ -53,19 +53,19 @@ use std::sync::atomic::{AtomicU8, Ordering};
 
 use rayon::prelude::*;
 
-use obikseq::CanonicalKmer;
 use obikindex::layer::meta::PartitionMeta;
+use obikseq::CanonicalKmer;
 use obipipeline::{ThrottleGuard, throttle};
 
-use obikindex::{OKIError, OKIResult};
 use obikindex::KmerIndex;
+use obikindex::{OKIError, OKIResult};
 
 use obikindex::layer::Layer;
 
 use super::cache::PartitionCache;
 use super::helpers::central_base;
 use super::iter::{SiblingEntry, SiblingLayerExt};
-use super::{olm_to_ok, FamilyMask, SiblingAnnex, ANNEX_FILE_NAME};
+use super::{ANNEX_FILE_NAME, FamilyMask, SiblingAnnex, olm_to_ok};
 
 /// Families per batch — see the module docs for the memory-vs-per-partition-
 /// density trade-off this picks a point on. At ~90 genomes and a few
@@ -191,14 +191,22 @@ pub(super) fn scan_layer_families(
     selection: &Selection,
     mut on_family: impl FnMut(usize, FamilyMask, &[u8]),
 ) -> OKIResult<()> {
-    let index_dir = layer_dir.parent().expect("layer_dir has a parent index dir");
+    let index_dir = layer_dir
+        .parent()
+        .expect("layer_dir has a parent index dir");
     let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
     let annex = Arc::new(SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?);
 
     let mat = Layer::open(layer_dir, &meta.mode, with_counts).map_err(olm_to_ok)?;
     let n_cols = mat.n_cols().min(n_genomes);
 
-    let ctx = Arc::new(LayerCtx { mat, n_parts, n_genomes, n_cols, k });
+    let ctx = Arc::new(LayerCtx {
+        mat,
+        n_parts,
+        n_genomes,
+        n_cols,
+        k,
+    });
 
     // Streamed straight from `iter_minorants_batch` (zips this layer's own
     // `iter_kmers()` with the annex, both in iteration order — never an
@@ -209,11 +217,14 @@ pub(super) fn scan_layer_families(
     // (see the module docs). `.scan()` computes each batch's starting
     // family index lazily, mirroring what the eager `chunks()`+running
     // `offset` used to do.
-    let batches = ctx.mat.iter_minorants_batch(annex, FAMILY_BATCH).scan(0usize, |offset, batch| {
-        let start = *offset;
-        *offset += batch.len();
-        Some((start, batch))
-    });
+    let batches =
+        ctx.mat
+            .iter_minorants_batch(annex, FAMILY_BATCH)
+            .scan(0usize, |offset, batch| {
+                let start = *offset;
+                *offset += batch.len();
+                Some((start, batch))
+            });
 
     let n_workers = obisys::effective_parallelism();
     let capacity = 4;
@@ -288,7 +299,7 @@ pub(super) fn scan_layer_families(
                 // — a pure MPHF lookup, no evidence check, since these are
                 // this layer's own kmers, known members by construction.
                 let kmers: Vec<CanonicalKmer> = batch.entries.iter().map(|e| e.kmer).collect();
-                let slots = ctx.mat.index_batch(&kmers);
+                let slots = ctx.mat.hash_batch(&kmers);
                 let mut carries: Vec<Vec<bool>> = (0..ctx.n_cols).map(|_| Vec::new()).collect();
                 ctx.mat.fill_sub_matrix_carries(&slots, &mut carries);
                 for (g, col) in carries.iter().enumerate() {
@@ -321,18 +332,24 @@ pub(super) fn scan_layer_families(
             // (one batch at a time, never several concurrently — see the
             // module docs), each thread owning one partition's queries
             // contiguously until this batch is done.
-            let genome_mask: Vec<AtomicU8> = batch.genome_mask.into_iter().map(AtomicU8::new).collect();
+            let genome_mask: Vec<AtomicU8> =
+                batch.genome_mask.into_iter().map(AtomicU8::new).collect();
             let fast_mode = cache.fast_mode();
-            batch.outgoing.par_iter().enumerate().filter(|(_, q)| !q.is_empty()).for_each(|(dest, queries)| {
-                let on_hit = |i: usize, base: u8, g: usize| {
-                    genome_mask[i * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
-                };
-                if fast_mode {
-                    cache.find_presence_batch_fast(dest, queries, n_genomes, on_hit);
-                } else {
-                    cache.find_presence_batch(dest, queries, n_genomes, on_hit);
-                }
-            });
+            batch
+                .outgoing
+                .par_iter()
+                .enumerate()
+                .filter(|(_, q)| !q.is_empty())
+                .for_each(|(dest, queries)| {
+                    let on_hit = |i: usize, base: u8, g: usize| {
+                        genome_mask[i * n_genomes + g].fetch_or(1 << base, Ordering::Relaxed);
+                    };
+                    if fast_mode {
+                        cache.find_presence_batch_fast(dest, queries, n_genomes, on_hit);
+                    } else {
+                        cache.find_presence_batch(dest, queries, n_genomes, on_hit);
+                    }
+                });
 
             for i in 0..n {
                 let family_idx = batch.start_family_idx + i;
@@ -347,7 +364,10 @@ pub(super) fn scan_layer_families(
             next_expected += n;
         }
     }
-    debug_assert!(pending.is_empty(), "every generated batch must have been replayed");
+    debug_assert!(
+        pending.is_empty(),
+        "every generated batch must have been replayed"
+    );
 
     Ok(())
 }