refactor: switch indexing to IndexMode and update metadata

Replace EvidenceKind with IndexMode (Exact, Approx, Hybrid) across layer construction and query dispatch. Update PartitionMeta and LayerMeta serialization to centralize index-wide configuration. Add flexible push_layer overloads to LayeredMap for dynamic index expansion without full rebuilds. Improve UnitigFileReader to gracefully fallback to sequential scanning when indexes are missing, eliminating panics.

src/obikpartitionner/src/index_layer.rs

@@ -5,7 +5,7 @@ use cacheline_ef::{CachelineEf, CachelineEfVec};
 use epserde::prelude::*;
 use obicompactvec::{PersistentCompactIntMatrix, PersistentCompactIntVec};
 use obidebruinj::GraphDeBruijn;
-use obilayeredmap::{EvidenceKind, OLMError, layer::Layer};
+use obilayeredmap::{IndexMode, OLMError, layer::Layer};
 use obilayeredmap::meta::PartitionMeta;
 use obiskio::{SKError, SKFileMeta, SKFileReader};
 use ptr_hash::{PtrHash, bucket_fn::CubicEps, hash::Xx64};
@@ -44,7 +44,7 @@ impl KmerPartition {
         min_ab: u32,
         max_ab: Option<u32>,
         with_counts: bool,
-        evidence: &EvidenceKind,
+        mode: &IndexMode,
         block_bits: u8,
     ) -> Result<usize, SKError> {
         let part_dir = self.part_dir(i);
@@ -110,7 +110,7 @@ impl KmerPartition {
         uw.close()?;
 
         if with_counts {
-            Layer::<PersistentCompactIntMatrix>::build(&layer_dir, block_bits, evidence, |kmer| {
+            Layer::<PersistentCompactIntMatrix>::build(&layer_dir, block_bits, mode, |kmer| {
                 match (&mphf1_opt, &counts1_opt) {
                     (Some(mphf), Some(counts)) => counts.get(mphf.index(&kmer.raw())),
                     _ => 1,
@@ -118,13 +118,11 @@ impl KmerPartition {
             })
             .map_err(olm_to_sk)?;
         } else {
-            Layer::<()>::build(&layer_dir, block_bits, evidence).map_err(olm_to_sk)?;
+            Layer::<()>::build(&layer_dir, block_bits, mode).map_err(olm_to_sk)?;
         }
 
-        // Write meta.json in the index/ directory so LayeredMap::open works
-        // (e.g. for subsequent merge operations).
         let index_dir = layer_dir.parent().expect("layer_dir has a parent");
-        PartitionMeta { n_layers: 1 }.save(index_dir).map_err(olm_to_sk)?;
+        PartitionMeta { n_layers: 1, mode: mode.clone() }.save(index_dir).map_err(olm_to_sk)?;
 
         Ok(n_kmers)
     }

src/obikpartitionner/src/merge_layer.rs

@@ -9,7 +9,7 @@ use obicompactvec::{PersistentBitMatrix, PersistentBitMatrixBuilder,
                     PersistentCompactIntVecBuilder};
 use obikseq::CanonicalKmer;
 use obiskio::{SKError, SKResult, UnitigFileReader};
-use obilayeredmap::{EvidenceKind, Layer, LayeredMap, MphfLayer, OLMError};
+use obilayeredmap::{IndexMode, Layer, LayeredMap, MphfLayer, OLMError};
 use obilayeredmap::meta::PartitionMeta;
 
 use crate::partition::KmerPartition;
@@ -52,18 +52,17 @@ pub(crate) enum SrcLayerData {
 }
 
 impl SrcLayerData {
-    pub(crate) fn open(layer_dir: &Path, mode: MergeMode) -> SKResult<Self> {
+    pub(crate) fn open(layer_dir: &Path, merge_mode: MergeMode, index_mode: &IndexMode) -> SKResult<Self> {
         let presence_dir = layer_dir.join("presence");
         let counts_dir   = layer_dir.join("counts");
-        match mode {
+        match merge_mode {
             MergeMode::Presence => {
                 if presence_dir.exists() {
-                    let mphf = MphfLayer::open(layer_dir).map_err(olm_to_sk)?;
+                    let mphf = MphfLayer::open(layer_dir, index_mode).map_err(olm_to_sk)?;
                     let mat  = PersistentBitMatrix::open(&presence_dir).map_err(SKError::Io)?;
                     Ok(SrcLayerData::Presence(mphf, mat))
                 } else if counts_dir.exists() {
-                    // Source is a count index; treat count > 0 as present via ColBuilder::Bit.
+                    let mphf = MphfLayer::open(layer_dir, index_mode).map_err(olm_to_sk)?;
-                    let mphf = MphfLayer::open(layer_dir).map_err(olm_to_sk)?;
                     let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
                     Ok(SrcLayerData::Count(mphf, mat))
                 } else {
@@ -72,7 +71,7 @@ impl SrcLayerData {
             }
             MergeMode::Count => {
                 if counts_dir.exists() {
-                    let mphf = MphfLayer::open(layer_dir).map_err(olm_to_sk)?;
+                    let mphf = MphfLayer::open(layer_dir, index_mode).map_err(olm_to_sk)?;
                     let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
                     Ok(SrcLayerData::Count(mphf, mat))
                 } else {
@@ -116,7 +115,7 @@ fn load_meta(dir: &Path) -> SKResult<PartitionMeta> {
         Err(e) if matches!(e, OLMError::Io(ref io_e) if io_e.kind() == std::io::ErrorKind::NotFound) => {
             let mut n = 0usize;
             while dir.join(format!("layer_{n}")).exists() { n += 1; }
-            let m = PartitionMeta { n_layers: n };
+            let m = PartitionMeta { n_layers: n, mode: IndexMode::default() };
             m.save(dir).map_err(olm_to_sk)?;
             Ok(m)
         }
@@ -217,12 +216,12 @@ impl KmerPartition {
                 uw.write(&unitig)?;
             }
             uw.close()?;
-            Layer::<()>::build(&new_layer_dir, block_bits, &EvidenceKind::Exact).map_err(olm_to_sk)?;
+            Layer::<()>::build(&new_layer_dir, block_bits, &IndexMode::Exact).map_err(olm_to_sk)?;
         }
         drop(g);
 
         let new_mphf = if any_new {
-            Some(MphfLayer::open(&new_layer_dir).map_err(olm_to_sk)?)
+            Some(MphfLayer::open(&new_layer_dir, &IndexMode::Exact).map_err(olm_to_sk)?)
         } else {
             None
         };
@@ -304,7 +303,7 @@ impl KmerPartition {
             for l in 0..src_meta.n_layers {
                 let src_layer_dir = src_index_dir.join(format!("layer_{l}"));
                 let reader = UnitigFileReader::open_sequential(&src_layer_dir.join("unitigs.bin"))?;
-                let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
+                let src_data = SrcLayerData::open(&src_layer_dir, mode, &src_meta.mode)?;
 
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                     let values = src_data.lookup(kmer, *src_n);

src/obikpartitionner/src/rebuild_layer.rs

@@ -8,7 +8,7 @@ use obicompactvec::{PersistentBitMatrixBuilder,
                     PersistentCompactIntVecBuilder};
 use obidebruinj::GraphDeBruijn;
 use obiskio::{SKError, SKResult, UnitigFileReader};
-use obilayeredmap::{EvidenceKind, Layer, MphfLayer, OLMError};
+use obilayeredmap::{IndexMode, Layer, MphfLayer, OLMError};
 use obilayeredmap::meta::PartitionMeta;
 
 use crate::filter::KmerFilter;

src/obilayeredmap/src/layer.rs

@@ -10,7 +10,7 @@ use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileReader, UnitigFileWriter};
 
 use crate::error::{OLMError, OLMResult};
-use crate::meta::EvidenceKind;
+use crate::meta::IndexMode;
 use crate::mphf_layer::MphfLayer;
 pub(crate) use crate::mphf_layer::UNITIGS_FILE;
 
@@ -62,8 +62,8 @@ pub struct Hit<T = ()> {
 // ── Common read path ──────────────────────────────────────────────────────────
 
 impl<D: LayerData> Layer<D> {
-    pub fn open(path: &Path) -> OLMResult<Self> {
+    pub fn open(path: &Path, mode: &IndexMode) -> OLMResult<Self> {
-        let mphf = MphfLayer::open(path)?;
+        let mphf = MphfLayer::open(path, mode)?;
         let data = D::open(path)?;
         Ok(Self { mphf, data })
     }
@@ -92,18 +92,13 @@ impl<D: LayerData> Layer<D> {
         MphfLayer::build_approx_evidence(layer_dir, b, z)
     }
 
-    /// Dispatch to `build_exact_evidence` or `build_approx_evidence`.
-    /// `block_bits` is forwarded to exact evidence only.
-    pub fn build_evidence(layer_dir: &Path, kind: &EvidenceKind, block_bits: u8) -> OLMResult<usize> {
-        MphfLayer::build_evidence(layer_dir, kind, block_bits)
-    }
 }
 
 // ── Mode 1 — set membership ───────────────────────────────────────────────────
 
 impl Layer<()> {
-    pub fn build(out_dir: &Path, block_bits: u8, evidence_kind: &EvidenceKind) -> OLMResult<usize> {
+    pub fn build(out_dir: &Path, block_bits: u8, mode: &IndexMode) -> OLMResult<usize> {
-        MphfLayer::build(out_dir, block_bits, evidence_kind, &mut |_, _| Ok(()))
+        MphfLayer::build(out_dir, block_bits, mode, &mut |_, _| Ok(()))
     }
 
     /// Create a presence matrix for a set-membership layer (first merge).
@@ -126,7 +121,7 @@ impl Layer<PersistentCompactIntMatrix> {
     pub fn build(
         out_dir: &Path,
         block_bits: u8,
-        evidence_kind: &EvidenceKind,
+        mode: &IndexMode,
         count_of: impl Fn(CanonicalKmer) -> u32,
     ) -> OLMResult<usize> {
         let n = UnitigFileReader::open_sequential(&out_dir.join(UNITIGS_FILE))?.n_kmers();
@@ -134,7 +129,7 @@ impl Layer<PersistentCompactIntMatrix> {
         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, evidence_kind, &mut |slot, kmer| {
+        let n_built = MphfLayer::build(out_dir, block_bits, mode, &mut |slot, kmer| {
             col.set(slot, count_of(kmer));
             Ok(())
         })?;
@@ -146,10 +141,10 @@ impl Layer<PersistentCompactIntMatrix> {
     pub fn build_from_map(
         out_dir: &Path,
         block_bits: u8,
-        evidence_kind: &EvidenceKind,
+        mode: &IndexMode,
         counts: &HashMap<CanonicalKmer, u32>,
     ) -> OLMResult<usize> {
-        Self::build(out_dir, block_bits, evidence_kind, |kmer| counts.get(&kmer).copied().unwrap_or(0))
+        Self::build(out_dir, block_bits, mode, |kmer| counts.get(&kmer).copied().unwrap_or(0))
     }
 }
 
@@ -179,7 +174,7 @@ impl Layer<PersistentBitMatrix> {
     pub fn build_presence(
         out_dir: &Path,
         block_bits: u8,
-        evidence_kind: &EvidenceKind,
+        mode: &IndexMode,
         n_genomes: usize,
         present_in: impl Fn(CanonicalKmer, usize) -> bool,
     ) -> OLMResult<usize> {
@@ -189,7 +184,7 @@ impl Layer<PersistentBitMatrix> {
         let mut cols: Vec<_> = (0..n_genomes)
             .map(|_| mb.add_col().map_err(OLMError::Io))
             .collect::<OLMResult<_>>()?;
-        let n_built = MphfLayer::build(out_dir, block_bits, evidence_kind, &mut |slot, kmer| {
+        let n_built = MphfLayer::build(out_dir, block_bits, mode, &mut |slot, kmer| {
             for (g, col) in cols.iter_mut().enumerate() {
                 col.set(slot, present_in(kmer, g));
             }

src/obilayeredmap/src/lib.rs

@@ -11,5 +11,5 @@ pub use error::{OLMError, OLMResult};
 pub use layer::{Hit, Layer, LayerData};
 pub use layered_store::LayeredStore;
 pub use map::LayeredMap;
-pub use meta::{EvidenceKind, LayerMeta};
+pub use meta::{IndexMode, PartitionMeta};
 pub use mphf_layer::MphfLayer;

src/obilayeredmap/src/map.rs

@@ -5,11 +5,10 @@ use std::path::{Path, PathBuf};
 use obicompactvec::PersistentCompactIntMatrix;
 use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileWriter, DEFAULT_BLOCK_BITS};
-use crate::meta::EvidenceKind;
 
 use crate::error::OLMResult;
 use crate::layer::{Hit, Layer, LayerData};
-use crate::meta::PartitionMeta;
+use crate::meta::{IndexMode, PartitionMeta};
 
 /// Layered kmer index for a single partition.
 ///
@@ -17,8 +16,8 @@ use crate::meta::PartitionMeta;
 /// the first match wins. Adding a dataset appends a new layer without
 /// rebuilding existing ones.
 pub struct LayeredMap<D: LayerData = ()> {
-    root: PathBuf,
+    root:   PathBuf,
-    meta: PartitionMeta,
+    meta:   PartitionMeta,
     layers: Vec<Layer<D>>,
 }
 
@@ -26,39 +25,26 @@ pub struct LayeredMap<D: LayerData = ()> {
 
 impl<D: LayerData> LayeredMap<D> {
     /// Open an existing layered index at `root`.
+    /// The mode is read once from `PartitionMeta` and applied to all layers.
     pub fn open(root: &Path) -> OLMResult<Self> {
         let meta = PartitionMeta::load(root)?;
         let layers = (0..meta.n_layers)
-            .map(|i| Layer::<D>::open(&layer_dir(root, i)))
+            .map(|i| Layer::<D>::open(&layer_dir(root, i), &meta.mode))
             .collect::<OLMResult<Vec<_>>>()?;
-        Ok(Self {
+        Ok(Self { root: root.to_owned(), meta, layers })
-            root: root.to_owned(),
-            meta,
-            layers,
-        })
     }
 
-    /// Create a new, empty layered index at `root`.
+    /// Create a new, empty layered index at `root` with the given mode.
-    pub fn create(root: &Path) -> OLMResult<Self> {
+    pub fn create(root: &Path, mode: IndexMode) -> OLMResult<Self> {
         fs::create_dir_all(root)?;
-        let meta = PartitionMeta::new();
+        let meta = PartitionMeta::new(mode);
         meta.save(root)?;
-        Ok(Self {
+        Ok(Self { root: root.to_owned(), meta, layers: Vec::new() })
-            root: root.to_owned(),
-            meta,
-            layers: Vec::new(),
-        })
     }
 
-    /// Return the number of layers in this index.
+    pub fn n_layers(&self) -> usize { self.layers.len() }
-    pub fn n_layers(&self) -> usize {
+    pub fn layer(&self, i: usize) -> &Layer<D> { &self.layers[i] }
-        self.layers.len()
+    pub fn mode(&self) -> &IndexMode { &self.meta.mode }
-    }
-
-    /// Return a reference to the `i`-th layer.
-    pub fn layer(&self, i: usize) -> &Layer<D> {
-        &self.layers[i]
-    }
 
     /// Query `kmer` across all layers. Returns `(layer_index, Hit)` on match.
     pub fn query(&self, kmer: CanonicalKmer) -> Option<(usize, Hit<D::Item>)> {
@@ -68,17 +54,15 @@ impl<D: LayerData> LayeredMap<D> {
             .find_map(|(i, layer)| layer.query(kmer).map(|hit| (i, hit)))
     }
 
-    /// Return a `UnitigFileWriter` for the next layer to be built.
     pub fn next_layer_writer(&self) -> OLMResult<UnitigFileWriter> {
         let dir = layer_dir(&self.root, self.layers.len());
         Layer::<D>::unitig_writer(&dir)
     }
 
-    /// Append a new layer to the index.
     fn append_layer(&mut self) -> OLMResult<()> {
         let i = self.layers.len();
         let dir = layer_dir(&self.root, i);
-        self.layers.push(Layer::<D>::open(&dir)?);
+        self.layers.push(Layer::<D>::open(&dir, &self.meta.mode)?);
         self.meta.n_layers = self.layers.len();
         self.meta.save(&self.root)?;
         Ok(())
@@ -91,7 +75,7 @@ impl LayeredMap<()> {
     pub fn push_layer(&mut self) -> OLMResult<usize> {
         let i = self.layers.len();
         let dir = layer_dir(&self.root, i);
-        Layer::<()>::build(&dir, DEFAULT_BLOCK_BITS, &EvidenceKind::Exact)?;
+        Layer::<()>::build(&dir, DEFAULT_BLOCK_BITS, &self.meta.mode)?;
         self.append_layer()?;
         Ok(i)
     }
@@ -103,15 +87,12 @@ impl LayeredMap<PersistentCompactIntMatrix> {
     pub fn push_layer(&mut self, count_of: impl Fn(CanonicalKmer) -> u32) -> OLMResult<usize> {
         let i = self.layers.len();
         let dir = layer_dir(&self.root, i);
-        Layer::<PersistentCompactIntMatrix>::build(&dir, DEFAULT_BLOCK_BITS, &EvidenceKind::Exact, count_of)?;
+        Layer::<PersistentCompactIntMatrix>::build(&dir, DEFAULT_BLOCK_BITS, &self.meta.mode, count_of)?;
         self.append_layer()?;
         Ok(i)
     }
 
-    pub fn push_layer_from_map(
+    pub fn push_layer_from_map(&mut self, counts: &HashMap<CanonicalKmer, u32>) -> OLMResult<usize> {
-        &mut self,
-        counts: &HashMap<CanonicalKmer, u32>,
-    ) -> OLMResult<usize> {
         self.push_layer(|kmer| counts.get(&kmer).copied().unwrap_or(0))
     }
 }

src/obilayeredmap/src/meta.rs

@@ -5,65 +5,45 @@ use serde::{Deserialize, Serialize};
 
 use crate::error::OLMResult;
 
-const META_FILE:       &str = "meta.json";
+const META_FILE: &str = "meta.json";
-const LAYER_META_FILE: &str = "layer_meta.json";
 
-// ── Layer-level metadata ──────────────────────────────────────────────────────
+// ── IndexMode ─────────────────────────────────────────────────────────────────
 
-/// Describes the evidence bundle stored alongside the MPHF for one layer.
+/// Evidence mode for an entire partitioned index — homogeneous across all layers.
+///
+/// Determined once at build time; stored in `PartitionMeta` (`meta.json`).
+/// All layers within an index share the same mode.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 #[serde(tag = "type", rename_all = "snake_case")]
-pub enum EvidenceKind {
+pub enum IndexMode {
     /// Exact evidence: `evidence.bin` + `unitigs.bin.idx`.  Zero false positives.
     Exact,
     /// Approximate evidence: `fingerprint.bin` only.
-    /// `b` — fingerprint bits; false-positive rate per k-mer query = 1/2^b.
+    /// `b` — fingerprint bits per slot; false-positive rate ≈ 1/2^b per query.
-    /// `z` — consecutive k-mers that must all match (Findere trick);
+    /// `z` — Findere consecutive-kmer parameter (build-time only; not used at query time).
-    ///        effective FP rate per sequencing read ≈ W / 2^(b·z)
-    ///        where W = L - k - z + 2 is the number of windows in a read of length L.
     Approx { b: u8, z: u8 },
+    /// Hybrid: both `fingerprint.bin` and `evidence.bin` + `unitigs.bin.idx`.
+    /// `find()` uses the fingerprint (O(1), approx); `find_strict()` uses exact evidence.
+    Hybrid { b: u8, z: u8 },
 }
 
-#[derive(Debug, Clone, Serialize, Deserialize)]
+impl Default for IndexMode {
-pub struct LayerMeta {
-    pub evidence: EvidenceKind,
-}
-
-impl Default for EvidenceKind {
     fn default() -> Self { Self::Exact }
 }
 
-impl LayerMeta {
+// ── PartitionMeta ─────────────────────────────────────────────────────────────
-    pub fn exact() -> Self {
-        Self { evidence: EvidenceKind::Exact }
-    }
-
-    pub fn approx(b: u8, z: u8) -> Self {
-        Self { evidence: EvidenceKind::Approx { b, z } }
-    }
-
-    pub fn load(layer_dir: &Path) -> OLMResult<Self> {
-        let f = File::open(layer_dir.join(LAYER_META_FILE))?;
-        Ok(serde_json::from_reader(f)?)
-    }
-
-    pub fn save(&self, layer_dir: &Path) -> OLMResult<()> {
-        let f = File::create(layer_dir.join(LAYER_META_FILE))?;
-        serde_json::to_writer_pretty(f, self)?;
-        Ok(())
-    }
-}
-
-// ── Partition-level metadata ──────────────────────────────────────────────────
 
+/// Index-level metadata stored in `meta.json` at the root of a partition index.
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct PartitionMeta {
     pub n_layers: usize,
+    #[serde(default)]
+    pub mode: IndexMode,
 }
 
 impl PartitionMeta {
-    pub fn new() -> Self {
+    pub fn new(mode: IndexMode) -> Self {
-        Self { n_layers: 0 }
+        Self { n_layers: 0, mode }
     }
 
     pub fn load(dir: &Path) -> OLMResult<Self> {
@@ -79,5 +59,5 @@ impl PartitionMeta {
 }
 
 impl Default for PartitionMeta {
-    fn default() -> Self { Self::new() }
+    fn default() -> Self { Self::new(IndexMode::Exact) }
 }

src/obilayeredmap/src/mphf_layer.rs

@@ -1,5 +1,5 @@
 use std::fs;
-use std::path::Path;
+use std::path::{Path, PathBuf};
 
 use cacheline_ef::{CachelineEf, CachelineEfVec};
 use epserde::prelude::*;
@@ -10,7 +10,7 @@ use ptr_hash::{PtrHash, PtrHashParams, bucket_fn::CubicEps, hash::Xx64};
 use crate::error::{OLMError, OLMResult};
 use crate::evidence::{Evidence, EvidenceWriter};
 use crate::fingerprint::{FingerprintVec, FingerprintVecWriter};
-use crate::meta::{EvidenceKind, LayerMeta};
+use crate::meta::IndexMode;
 
 pub(crate) const MPHF_FILE:        &str = "mphf.bin";
 pub(crate) const UNITIGS_FILE:     &str = "unitigs.bin";
@@ -19,19 +19,22 @@ pub(crate) const FINGERPRINT_FILE: &str = "fingerprint.bin";
 
 pub(crate) type Mphf = PtrHash<u64, CubicEps, CachelineEfVec<Vec<CachelineEf>>, Xx64, Vec<u8>>;
 
-// ── Evidence store ────────────────────────────────────────────────────────────
+// ── LayerEvidence ─────────────────────────────────────────────────────────────
 
 enum LayerEvidence {
-    Exact { evidence: Evidence, unitigs: UnitigFileReader },
+    Exact  { evidence: Evidence, unitigs: UnitigFileReader },
-    Approx { fingerprint: FingerprintVec },
+    Approx { fingerprint: FingerprintVec, unitigs_path: PathBuf },
+    Hybrid { evidence: Evidence, unitigs: UnitigFileReader, fingerprint: FingerprintVec },
 }
 
 // ── MphfLayer ─────────────────────────────────────────────────────────────────
 
 /// Autonomous kmer → slot mapping for one layer.
 ///
-/// Dispatches queries to exact or approximate evidence transparently based on
+/// Two query methods:
-/// the `layer_meta.json` written at build time.
+/// - [`find`](Self::find) — O(1), uses fingerprint (Approx/Hybrid) or exact evidence (Exact).
+/// - [`find_strict`](Self::find_strict) — always exact; O(1) on Exact/Hybrid layers,
+///   O(n) sequential scan on Approx layers.
 pub struct MphfLayer {
     mphf: Mphf,
     ev:   LayerEvidence,
@@ -39,21 +42,31 @@ pub struct MphfLayer {
 }
 
 impl MphfLayer {
-    pub fn open(dir: &Path) -> OLMResult<Self> {
+    /// Open a layer using the index-level `mode` determined at `LayeredMap` open time.
-        let meta = LayerMeta::load(dir)?;
+    /// No per-layer metadata file is read.
+    pub fn open(dir: &Path, mode: &IndexMode) -> OLMResult<Self> {
         let mphf: Mphf = Mphf::load_full(&dir.join(MPHF_FILE))
             .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
-        let (ev, n) = match meta.evidence {
+        let (ev, n) = match mode {
-            EvidenceKind::Exact => {
+            IndexMode::Exact => {
                 let evidence = Evidence::open(&dir.join(EVIDENCE_FILE))?;
                 let n = evidence.len();
+                // open() auto-detects: uses direct access since exact layers always have .idx
                 let unitigs = UnitigFileReader::open(&dir.join(UNITIGS_FILE))?;
                 (LayerEvidence::Exact { evidence, unitigs }, n)
             }
-            EvidenceKind::Approx { .. } => {
+            IndexMode::Approx { .. } => {
                 let fingerprint = FingerprintVec::open(&dir.join(FINGERPRINT_FILE))?;
                 let n = fingerprint.n();
-                (LayerEvidence::Approx { fingerprint }, n)
+                let unitigs_path = dir.join(UNITIGS_FILE);
+                (LayerEvidence::Approx { fingerprint, unitigs_path }, n)
+            }
+            IndexMode::Hybrid { .. } => {
+                let evidence    = Evidence::open(&dir.join(EVIDENCE_FILE))?;
+                let fingerprint = FingerprintVec::open(&dir.join(FINGERPRINT_FILE))?;
+                let n = evidence.len();
+                let unitigs = UnitigFileReader::open(&dir.join(UNITIGS_FILE))?;
+                (LayerEvidence::Hybrid { evidence, unitigs, fingerprint }, n)
             }
         };
         Ok(Self { mphf, ev, n })
@@ -61,45 +74,60 @@ impl MphfLayer {
 
     // ── Query API ─────────────────────────────────────────────────────────────
 
-    /// Transparent dispatch: routes to `find_exact` or `find_approx` based on
+    /// O(1) lookup — dispatches automatically:
-    /// the evidence loaded at `open` time.
+    /// - Exact:  evidence + `verify_canonical_kmer`, zero false positives.
+    /// - Approx: fingerprint check, false-positive rate ≈ 1/2^b.
+    /// - Hybrid: fingerprint check (fast path), zero false positives via `find_strict`.
     #[inline]
     pub fn find(&self, kmer: CanonicalKmer) -> Option<usize> {
+        let slot = self.mphf.index(&kmer.raw());
+        if slot >= self.n { return None; }
         match &self.ev {
-            LayerEvidence::Exact { .. }  => self.find_exact(kmer),
+            LayerEvidence::Exact { evidence, unitigs } => {
-            LayerEvidence::Approx { .. } => self.find_approx(kmer),
+                let (chunk_id, rank) = evidence.decode(slot);
+                if unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
+                    Some(slot)
+                } else {
+                    None
+                }
+            }
+            LayerEvidence::Approx { fingerprint, .. } |
+            LayerEvidence::Hybrid { fingerprint, .. } => {
+                if fingerprint.matches(slot, kmer.seq_hash()) { Some(slot) } else { None }
+            }
         }
     }
 
-    /// Exact lookup: zero false positives.  Panics if the layer was opened with
+    /// Always-exact lookup — zero false positives regardless of mode.
-    /// approximate evidence.
+    ///
-    #[inline]
+    /// - Exact/Hybrid: O(1) via evidence + `verify_canonical_kmer`.
-    pub fn find_exact(&self, kmer: CanonicalKmer) -> Option<usize> {
+    /// - Approx: O(n) sequential scan of `unitigs.bin` to confirm the kmer
-        let LayerEvidence::Exact { evidence, unitigs } = &self.ev else {
+    ///   that owns the slot, then exact comparison.
-            panic!("find_exact called on an approximate layer");
+    pub fn find_strict(&self, kmer: CanonicalKmer) -> Option<usize> {
-        };
         let slot = self.mphf.index(&kmer.raw());
         if slot >= self.n { return None; }
-        let (chunk_id, rank) = evidence.decode(slot);
+        match &self.ev {
-        if unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
+            LayerEvidence::Exact  { evidence, unitigs } |
-            Some(slot)
+            LayerEvidence::Hybrid { evidence, unitigs, .. } => {
-        } else {
+                let (chunk_id, rank) = evidence.decode(slot);
-            None
+                if unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
+                    Some(slot)
+                } else {
+                    None
+                }
+            }
+            LayerEvidence::Approx { unitigs_path, .. } => {
+                let reader = UnitigFileReader::open_sequential(unitigs_path).ok()?;
+                for stored in reader.iter_canonical_kmers() {
+                    if self.mphf.index(&stored.raw()) == slot {
+                        return if stored == kmer { Some(slot) } else { None };
+                    }
+                }
+                None
+            }
         }
     }
 
-    /// Approximate lookup: false-positive rate 1/2^b per k-mer query.  Panics
-    /// if the layer was opened with exact evidence.
-    #[inline]
-    pub fn find_approx(&self, kmer: CanonicalKmer) -> Option<usize> {
-        let LayerEvidence::Approx { fingerprint } = &self.ev else {
-            panic!("find_approx called on an exact layer");
-        };
-        let slot = self.mphf.index(&kmer.raw());
-        if slot >= self.n { return None; }
-        if fingerprint.matches(slot, kmer.seq_hash()) { Some(slot) } else { None }
-    }
-
     pub fn n(&self) -> usize { self.n }
 
     // ── Build helpers ─────────────────────────────────────────────────────────
@@ -109,19 +137,7 @@ impl MphfLayer {
         Ok(UnitigFileWriter::create(&dir.join(UNITIGS_FILE))?)
     }
 
-    /// Dispatch to `build_exact_evidence` or `build_approx_evidence` based on
-    /// `kind`.  `block_bits` is forwarded to exact evidence only.
-    pub fn build_evidence(dir: &Path, kind: &EvidenceKind, block_bits: u8) -> OLMResult<usize> {
-        match kind {
-            EvidenceKind::Exact           => Self::build_exact_evidence(dir, block_bits),
-            EvidenceKind::Approx { b, z } => Self::build_approx_evidence(dir, *b, *z),
-        }
-    }
-
     /// Build `evidence.bin` + `unitigs.bin.idx` from `unitigs.bin` + `mphf.bin`.
-    ///
-    /// `block_bits` controls the `.idx` block size (2^block_bits chunks per block).
-    /// Uses sequential iteration — no `.idx` required on entry.
     pub fn build_exact_evidence(dir: &Path, block_bits: u8) -> OLMResult<usize> {
         let unitig_path = dir.join(UNITIGS_FILE);
         let unitigs = UnitigFileReader::open_sequential(&unitig_path)?;
@@ -130,7 +146,6 @@ impl MphfLayer {
         if n == 0 {
             fs::File::create(dir.join(EVIDENCE_FILE))?;
             build_unitig_idx(&unitig_path, block_bits)?;
-            LayerMeta::exact().save(dir)?;
             return Ok(0);
         }
 
@@ -156,13 +171,10 @@ impl MphfLayer {
 
         ev.write(&dir.join(EVIDENCE_FILE))?;
         build_unitig_idx(&unitig_path, block_bits)?;
-        LayerMeta::exact().save(dir)?;
         Ok(n)
     }
 
     /// Build `fingerprint.bin` from `unitigs.bin` + `mphf.bin`.
-    /// `b` — fingerprint bits (1..=64); `z` — Findere consecutive k-mer
-    /// parameter (≥1).  No `.idx` is written.
     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()));
@@ -176,7 +188,6 @@ impl MphfLayer {
 
         if n == 0 {
             FingerprintVecWriter::new(0, b).write(&dir.join(FINGERPRINT_FILE))?;
-            LayerMeta::approx(b, z).save(dir)?;
             return Ok(0);
         }
 
@@ -194,139 +205,113 @@ impl MphfLayer {
         }
 
         fw.write(&dir.join(FINGERPRINT_FILE))?;
-        LayerMeta::approx(b, z).save(dir)?;
         Ok(n)
     }
 
-    /// Build MPHF then evidence from the unitigs file already present in `dir`.
+    /// Build MPHF + evidence from `unitigs.bin` already present in `dir`.
     ///
-    /// - Exact: `.idx` is built for pass-1 parallel construction and kept for
+    /// `fill_slot(slot, kmer)` is called once per kmer in all modes.
-    ///   query-time kmer verification.  `evidence.bin` is written.
+    /// No `layer_meta.json` is written — the mode is an index-level property
-    /// - Approx: pass-1 uses `open_sequential` + `par_bridge` — no `.idx` is
+    /// stored in `PartitionMeta`.
-    ///   ever created.  `fingerprint.bin` is written.
-    ///
-    /// `fill_slot(slot, kmer)` is called once per kmer in both modes.
     pub(crate) fn build(
         dir: &Path,
         block_bits: u8,
-        evidence_kind: &EvidenceKind,
+        mode: &IndexMode,
         fill_slot: &mut impl FnMut(usize, CanonicalKmer) -> OLMResult<()>,
     ) -> OLMResult<usize> {
         use rayon::prelude::*;
 
         let unitig_path = dir.join(UNITIGS_FILE);
+        let n = UnitigFileReader::open_sequential(&unitig_path)?.n_kmers();
 
-        match evidence_kind {
+        let sk_to_olm = |e: obiskio::SKError| match e {
-            // ── Exact path ────────────────────────────────────────────────────
+            obiskio::SKError::Io(io) => OLMError::Io(io),
-            // .idx is built LAST, once evidence.bin is written, so it is never
+            e => OLMError::InvalidLayer(e.to_string()),
-            // present during construction — only at query time.
+        };
-            EvidenceKind::Exact => {
-                let n = UnitigFileReader::open_sequential(&unitig_path)?.n_kmers();
-                let keys = CanonicalKmerIter::new(&unitig_path)
-                    .map_err(|e| match e {
-                        obiskio::SKError::Io(io) => OLMError::Io(io),
-                        e => OLMError::InvalidLayer(e.to_string()),
-                    })?;
 
-                if n == 0 {
+        // ── Empty layer ───────────────────────────────────────────────────────
+        if n == 0 {
+            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 {
+                IndexMode::Exact | IndexMode::Hybrid { .. } => {
                     fs::File::create(dir.join(EVIDENCE_FILE))?;
-                    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()))?;
-                    LayerMeta::exact().save(dir)?;
                     build_unitig_idx(&unitig_path, block_bits)?;
-                    return Ok(0);
                 }
+                IndexMode::Approx { b, .. } => {
+                    FingerprintVecWriter::new(0, *b).write(&dir.join(FINGERPRINT_FILE))?;
+                }
+            }
+            if let IndexMode::Hybrid { b, .. } = mode {
+                FingerprintVecWriter::new(0, *b).write(&dir.join(FINGERPRINT_FILE))?;
+            }
+            return Ok(0);
+        }
 
-                // Pass 1 — MPHF construction via clonable mmap iterator
+        // ── Pass 1: MPHF via clonable mmap iterator ───────────────────────────
-                let mphf: Mphf =
+        let keys = CanonicalKmerIter::new(&unitig_path).map_err(sk_to_olm)?;
-                    Mphf::new_from_par_iter(n, keys.map(|k| k.raw()).par_bridge(), PtrHashParams::<CubicEps>::default());
+        let mphf: Mphf =
-                mphf.store(&dir.join(MPHF_FILE))
+            Mphf::new_from_par_iter(n, keys.map(|k| k.raw()).par_bridge(),
-                    .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
+                                    PtrHashParams::<CubicEps>::default());
+        mphf.store(&dir.join(MPHF_FILE))
+            .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
 
-                // Pass 2 — sequential: fill evidence.bin + callback
+        // ── Pass 2: fill evidence files + callback ────────────────────────────
-                let unitigs2 = UnitigFileReader::open_sequential(&unitig_path)?;
+        let unitigs2 = UnitigFileReader::open_sequential(&unitig_path)?;
-                let mut ev   = EvidenceWriter::new(n);
+        let mut seen = vec![0u8; (n + 7) / 8];
-                let mut seen = vec![0u8; (n + 7) / 8];
 
+        match mode {
+            IndexMode::Exact => {
+                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 {
+                    if slot >= n { return Err(OLMError::Mphf("slot out of bounds".into())); }
-                        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())); }
-                    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)?;
                 }
-
                 ev.write(&dir.join(EVIDENCE_FILE))?;
-                LayerMeta::exact().save(dir)?;
-                // .idx built last: strictly for query-time kmer verification
                 build_unitig_idx(&unitig_path, block_bits)?;
-                Ok(n)
             }
 
-            // ── Approx path ───────────────────────────────────────────────────
+            IndexMode::Approx { b, .. } => {
-            // No .idx is created at any point.
+                let mut fw = FingerprintVecWriter::new(n, *b);
-            EvidenceKind::Approx { b, z } => {
-                let unitigs = UnitigFileReader::open_sequential(&unitig_path)?;
-                let n = unitigs.n_kmers();
-
-                if n == 0 {
-                    FingerprintVecWriter::new(0, *b).write(&dir.join(FINGERPRINT_FILE))?;
-                    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()))?;
-                    LayerMeta::approx(*b, *z).save(dir)?;
-                    return Ok(0);
-                }
-
-                // Pass 1 — MPHF construction via mmap-backed clonable iterator.
-                // No .idx is created. par_bridge() parallelises the sequential scan;
-                // Clone on CanonicalKmerRawIter shares the Arc<Mmap> and resets to pos 0.
-                let keys = CanonicalKmerIter::new(&unitig_path)
-                    .map_err(|e| match e {
-                        obiskio::SKError::Io(io) => OLMError::Io(io),
-                        e => OLMError::InvalidLayer(e.to_string()),
-                    })?;
-                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()))?;
-
-                // Pass 2 — sequential: fill fingerprint.bin + callback
-                let unitigs2 = UnitigFileReader::open_sequential(&unitig_path)?;
-                let mut fw   = FingerprintVecWriter::new(n, *b);
-                let mut seen = vec![0u8; (n + 7) / 8];
-
                 for kmer in unitigs2.iter_canonical_kmers() {
                     let slot = mphf.index(&kmer.raw());
-                    if slot >= n {
+                    if slot >= n { return Err(OLMError::Mphf("slot out of bounds".into())); }
-                        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())); }
-                    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)?;
                 }
-
                 fw.write(&dir.join(FINGERPRINT_FILE))?;
-                LayerMeta::approx(*b, *z).save(dir)?;
+            }
-                Ok(n)
+
+            IndexMode::Hybrid { b, .. } => {
+                let mut ev = EvidenceWriter::new(n);
+                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())); }
+                    seen[byte] |= bit;
+                    ev.set(slot, chunk_id as u32, rank as u8);
+                    fw.set(slot, kmer.seq_hash());
+                    fill_slot(slot, kmer)?;
+                }
+                ev.write(&dir.join(EVIDENCE_FILE))?;
+                fw.write(&dir.join(FINGERPRINT_FILE))?;
+                build_unitig_idx(&unitig_path, block_bits)?;
             }
         }
+
+        Ok(n)
     }
 }

src/obiskio/src/unitig_index.rs

@@ -198,11 +198,16 @@ pub fn build_unitig_idx(unitigs_path: &Path, block_bits: u8) -> SKResult<()> {
 
 // ── Reader ────────────────────────────────────────────────────────────────────
 
-/// Read-only random-access view of a unitig file.
+/// Memory-mapped view of a unitig file, with optional direct-access index.
 ///
-/// The sequence file is memory-mapped; the block offset table is loaded into RAM
+/// Three constructors select the operating mode:
-/// on open.  Random access to chunk `i`: O(1 << block_bits) sequential mmap
+/// - [`open`](Self::open) — smart default: direct access if `.idx` exists, sequential otherwise.
-/// reads.  Sequential iteration: O(n) via a running-offset cursor.
+/// - [`open_sequential`](Self::open_sequential) — always sequential, ignores `.idx`.
+/// - [`open_direct_access`](Self::open_direct_access) — requires `.idx`, errors if absent.
+///
+/// All positional methods (`chunk_start`, `verify_canonical_kmer`, …) work in
+/// both modes.  Without `.idx` they fall back to an O(i) sequential scan —
+/// correct but slower.
 pub struct UnitigFileReader {
     mmap:          Mmap,
     block_offsets: Vec<u32>,
@@ -214,8 +219,52 @@ pub struct UnitigFileReader {
 }
 
 impl UnitigFileReader {
-    /// Open with `.idx` — enables both sequential iteration and random access.
+    /// Smart default: opens with direct access if `.idx` is present, sequential otherwise.
     pub fn open(path: &Path) -> SKResult<Self> {
+        if idx_path(path).exists() {
+            Self::open_direct_access(path)
+        } else {
+            Self::open_sequential(path)
+        }
+    }
+
+    /// Always sequential — never reads `.idx` even if present.
+    ///
+    /// Scans the binary file once to count chunks and k-mers.
+    /// Positional access (`chunk_start`, `verify_canonical_kmer`) falls back to
+    /// O(i) sequential scan.
+    pub fn open_sequential(path: &Path) -> SKResult<Self> {
+        let file = File::open(path).map_err(SKError::Io)?;
+        let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
+        let k = obikseq::params::k();
+
+        let mut offset    = 0usize;
+        let mut n_unitigs = 0usize;
+        let mut n_kmers   = 0usize;
+        while offset < mmap.len() {
+            let seql_minus_k = mmap[offset] as usize;
+            n_kmers   += seql_minus_k + 1;
+            offset    += 1 + (seql_minus_k + k + 3) / 4;
+            n_unitigs += 1;
+        }
+
+        Ok(Self {
+            mmap,
+            block_offsets: Vec::new(),
+            n_unitigs,
+            n_kmers,
+            k,
+            block_bits: DEFAULT_BLOCK_BITS,
+            mask: (1usize << DEFAULT_BLOCK_BITS) - 1,
+        })
+    }
+
+    /// Requires `.idx` — errors if the companion index file is absent.
+    ///
+    /// Enables O(1 << block_bits) positional access to any chunk.
+    /// Use only when direct access is architecturally required (query-time
+    /// verification on an exact-evidence layer).
+    pub fn open_direct_access(path: &Path) -> SKResult<Self> {
         let file = File::open(path).map_err(SKError::Io)?;
         let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
         let (n_unitigs, n_kmers, block_bits, block_offsets) = read_idx(&idx_path(path))?;
@@ -231,58 +280,38 @@ impl UnitigFileReader {
         })
     }
 
-    /// Open without `.idx` — sequential iteration only, no random access.
-    ///
-    /// Scans the binary file once to count chunks and k-mers.  Use when only
-    /// [`Self::iter_kmers`], [`Self::iter_canonical_kmers`], or
-    /// [`Self::iter_indexed_canonical_kmers`] are needed.
-    pub fn open_sequential(path: &Path) -> SKResult<Self> {
-        let file = File::open(path).map_err(SKError::Io)?;
-        let mmap = unsafe { Mmap::map(&file).map_err(SKError::Io)? };
-        let k = obikseq::params::k();
-
-        let mut offset     = 0usize;
-        let mut n_unitigs  = 0usize;
-        let mut n_kmers    = 0usize;
-        while offset < mmap.len() {
-            let seql_minus_k = mmap[offset] as usize;
-            n_kmers  += seql_minus_k + 1;
-            offset   += 1 + (seql_minus_k + k + 3) / 4;
-            n_unitigs += 1;
-        }
-
-        Ok(Self {
-            mmap,
-            block_offsets: Vec::new(), // empty → random access disabled
-            n_unitigs,
-            n_kmers,
-            k,
-            block_bits: DEFAULT_BLOCK_BITS,
-            mask: (1usize << DEFAULT_BLOCK_BITS) - 1,
-        })
-    }
-
     pub fn len(&self) -> usize { self.n_unitigs }
     pub fn is_empty(&self) -> bool { self.n_unitigs == 0 }
     pub fn n_kmers(&self) -> usize { self.n_kmers }
     pub fn block_bits(&self) -> u8 { self.block_bits }
+    pub fn has_direct_access(&self) -> bool { !self.block_offsets.is_empty() }
 
-    /// Byte offset of the START of record `i` (the seql byte) in the mmap.
+    /// Byte offset of record `i` in the mmap.
+    ///
+    /// Fast path (O(1 << block_bits)) when `.idx` is loaded; degraded O(i)
+    /// sequential scan otherwise.
     #[inline]
     fn chunk_start(&self, i: usize) -> usize {
-        assert!(!self.block_offsets.is_empty(),
+        if !self.block_offsets.is_empty() {
-            "random access requires UnitigFileReader::open(); use open_sequential() for iteration only");
+            if self.block_bits == 0 {
-        if self.block_bits == 0 {
+                return self.block_offsets[i] as usize;
-            return self.block_offsets[i] as usize;
+            }
+            let block = i >> self.block_bits;
+            let rem   = i &  self.mask;
+            let mut offset = self.block_offsets[block] as usize;
+            for _ in 0..rem {
+                let seql_minus_k = self.mmap[offset] as usize;
+                offset += 1 + (seql_minus_k + self.k + 3) / 4;
+            }
+            offset
+        } else {
+            let mut offset = 0usize;
+            for _ in 0..i {
+                let seql_minus_k = self.mmap[offset] as usize;
+                offset += 1 + (seql_minus_k + self.k + 3) / 4;
+            }
+            offset
         }
-        let block = i >> self.block_bits;
-        let rem   = i &  self.mask;
-        let mut offset = self.block_offsets[block] as usize;
-        for _ in 0..rem {
-            let seql_minus_k = self.mmap[offset] as usize;
-            offset += 1 + (seql_minus_k + self.k + 3) / 4;
-        }
-        offset
     }
 
     /// Nucleotide length of chunk `i`.
@@ -307,7 +336,9 @@ impl UnitigFileReader {
         extract_kmer_raw(&self.mmap[offset + 1..], j, self.k)
     }
 
-    /// `true` iff the k-mer at position `j` of chunk `i` equals `query` (canonical).
+    /// `true` iff the k-mer at position `j` of chunk `i` matches `query`.
+    ///
+    /// Works in both modes; O(i) scan when `.idx` is absent.
     #[inline]
     pub fn verify_canonical_kmer(&self, i: usize, j: usize, query: CanonicalKmer) -> bool {
         canonical_raw(self.raw_kmer(i, j), self.k) == query.raw()