README.md

@@ -79,9 +79,12 @@ Non-ACGT characters act as hard breaks between k-mer segments in all formats.
 ## Quick start
 
 ```sh
-# Build an exact index for two genomes
+# Build an exact index for each genome independently
-obikmer index --kmer-size 31 --label genome_a genome_a.fa --output index/
+obikmer index --kmer-size 31 --label genome_a genome_a.fa --output index_a/
-obikmer index --kmer-size 31 --label genome_b genome_b.fa --output index/
+obikmer index --kmer-size 31 --label genome_b genome_b.fa --output index_b/
+
+# Merge into a single multi-genome index
+obikmer merge --output index/ index_a/ index_b/
 
 # Convert to approximate index (z=5, 8-bit fingerprints)
 obikmer reindex --approx -z 5 --evidence-bits 8 index/

src/obikindex/src/merge.rs

@@ -63,8 +63,15 @@ impl KmerIndex {
             }
         }
 
-        // ── Validate evidence compatibility ───────────────────────────────────
+        // ── Choose base: largest source in the output evidence mode ───────────
-        let evidence = validate_evidence_compat(sources)?;
+        let base_idx = choose_base(sources, mode);
+        let mut ordered: Vec<&KmerIndex> = Vec::with_capacity(sources.len());
+        ordered.push(sources[base_idx]);
+        for (i, &src) in sources.iter().enumerate() {
+            if i != base_idx { ordered.push(src); }
+        }
+        let sources: &[&KmerIndex] = &ordered;
+        let evidence = sources[0].meta.config.evidence.clone();
 
         // ── Compute final genome labels (rename duplicates if requested) ───────
         let (source_labels, all_genomes) = compute_labels(sources, rename_duplicates)?;
@@ -96,7 +103,7 @@ impl KmerIndex {
         let mut meta = IndexMeta::read(output).map_err(OKIError::Io)?;
         meta.genomes = all_genomes;
         meta.config.with_counts = mode == MergeMode::Count;
-        meta.config.evidence = evidence;
+        meta.config.evidence = evidence.clone();
         meta.write(output)?;
 
         // In presence/absence mode, purge counts/ directories inherited from
@@ -147,7 +154,7 @@ impl KmerIndex {
                 .filter_map(|i| {
                     let srcs: Vec<(&obikpartitionner::KmerPartition, usize)> =
                         remaining_sources.iter().map(|s| (&s.partition, s.meta.genomes.len())).collect();
-                    let result = dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes, block_bits).err();
+                    let result = dst_partition.merge_partition(i, &srcs, mode, n_dst_genomes, block_bits, &evidence).err();
                     pb.inc(1);
                     result
                 })
@@ -265,34 +272,51 @@ fn partition_bar(n: u64) -> ProgressBar {
     pb
 }
 
-/// Check that all sources share the same evidence kind.
+/// A source is "trivial" if its presence/count values carry no approximation:
+/// single-genome presence index (SetMembership — all values are 1 by construction).
+fn is_trivial(src: &KmerIndex, mode: MergeMode) -> bool {
+    src.meta.genomes.len() == 1 && mode == MergeMode::Presence
+}
+
+/// Sum of all `unitigs.bin` sizes across every partition and layer.
+/// Used as a proxy for the number of indexed smers.
+fn index_unitig_size(src: &KmerIndex) -> u64 {
+    let n = src.partition.n_partitions();
+    let mut total = 0u64;
+    for i in 0..n {
+        let index_dir = src.partition.part_dir(i).join("index");
+        let mut l = 0usize;
+        loop {
+            let p = index_dir.join(format!("layer_{l}")).join("unitigs.bin");
+            if !p.exists() { break; }
+            if let Ok(m) = std::fs::metadata(&p) { total += m.len(); }
+            l += 1;
+        }
+    }
+    total
+}
+
+/// Choose the index to use as bootstrap base.
 ///
-/// Rules:
+/// Rule — mieux-disant: if any non-trivial source uses approximate evidence
-/// - all `Exact`                        → OK, returns `Exact`
+/// (Approx or Hybrid), the output must also be approximate; the base must
-/// - all `Approx { b, z }` same params  → OK, returns `Approx { b, z }`
+/// therefore come from an approximate source so its layers carry the right
-/// - mixed exact/approx or different approx params → `IncompatibleEvidence`
+/// evidence files.  Among qualifying candidates, the largest (by unitig size)
-fn validate_evidence_compat(sources: &[&KmerIndex]) -> OKIResult<IndexMode> {
+/// is chosen to minimise the number of new smers in the merge layer.
-    let ref_ev = &sources[0].meta.config.evidence;
+fn choose_base(sources: &[&KmerIndex], mode: MergeMode) -> usize {
-    for src in &sources[1..] {
+    let needs_approx = sources.iter().any(|src| {
-        let ev = &src.meta.config.evidence;
+        !is_trivial(src, mode)
-        let compat = match (ref_ev, ev) {
+            && matches!(src.meta.config.evidence, IndexMode::Approx { .. } | IndexMode::Hybrid { .. })
-            (IndexMode::Exact, IndexMode::Exact) => true,
+    });
-            (IndexMode::Approx { b: b1, z: z1 },
+
-             IndexMode::Approx { b: b2, z: z2 }) => b1 == b2 && z1 == z2,
+    sources.iter().enumerate()
-            (IndexMode::Hybrid { b: b1, z: z1 },
+        .filter(|(_, src)| {
-             IndexMode::Hybrid { b: b2, z: z2 }) => b1 == b2 && z1 == z2,
+            !needs_approx
-            _ => false,
+                || matches!(src.meta.config.evidence, IndexMode::Approx { .. } | IndexMode::Hybrid { .. })
-        };
+        })
-        if !compat {
+        .max_by_key(|(_, src)| index_unitig_size(src))
-            return Err(OKIError::IncompatibleEvidence(format!(
+        .map(|(i, _)| i)
-                "source {:?} has evidence {:?}, expected {:?} — \
+        .unwrap()
-                 convert all sources to the same evidence kind first \
-                 (use the `reindex` command)",
-                src.root_path.display(), ev, ref_ev,
-            )));
-        }
-    }
-    Ok(ref_ev.clone())
 }
 
 fn copy_dir_all(src: &Path, dst: &Path) -> io::Result<()> {

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::{IndexMode, Layer, LayeredMap, MphfLayer, OLMError};
+use obilayeredmap::{IndexMode, Layer, LayeredMap, MphfOnly, OLMError};
 use obilayeredmap::meta::PartitionMeta;
 
 use crate::partition::KmerPartition;
@@ -47,22 +47,22 @@ impl ColBuilder {
 pub(crate) enum SrcLayerData {
     /// Pure set-membership layer (no data matrix): every kmer is present in all genomes.
     SetMembership,
-    Presence(MphfLayer, PersistentBitMatrix),
+    Presence(MphfOnly, PersistentBitMatrix),
-    Count(MphfLayer, PersistentCompactIntMatrix),
+    Count(MphfOnly, PersistentCompactIntMatrix),
 }
 
 impl SrcLayerData {
-    pub(crate) fn open(layer_dir: &Path, merge_mode: MergeMode, index_mode: &IndexMode) -> SKResult<Self> {
+    pub(crate) fn open(layer_dir: &Path, merge_mode: MergeMode) -> SKResult<Self> {
         let presence_dir = layer_dir.join("presence");
         let counts_dir   = layer_dir.join("counts");
         match merge_mode {
             MergeMode::Presence => {
                 if presence_dir.exists() {
-                    let mphf = MphfLayer::open(layer_dir, index_mode).map_err(olm_to_sk)?;
+                    let mphf = MphfOnly::open(layer_dir).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() {
-                    let mphf = MphfLayer::open(layer_dir, index_mode).map_err(olm_to_sk)?;
+                    let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
                     let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
                     Ok(SrcLayerData::Count(mphf, mat))
                 } else {
@@ -71,7 +71,7 @@ impl SrcLayerData {
             }
             MergeMode::Count => {
                 if counts_dir.exists() {
-                    let mphf = MphfLayer::open(layer_dir, index_mode).map_err(olm_to_sk)?;
+                    let mphf = MphfOnly::open(layer_dir).map_err(olm_to_sk)?;
                     let mat  = PersistentCompactIntMatrix::open(&counts_dir).map_err(SKError::Io)?;
                     Ok(SrcLayerData::Count(mphf, mat))
                 } else {
@@ -82,22 +82,16 @@ impl SrcLayerData {
     }
 
     /// Return one value per source genome for `kmer`.
+    /// The caller guarantees `kmer` is in the source MPHF domain.
+    #[inline]
     pub(crate) fn lookup(&self, kmer: CanonicalKmer, n_genomes: usize) -> Vec<u32> {
         match self {
             SrcLayerData::SetMembership => vec![1u32; n_genomes],
             SrcLayerData::Presence(mphf, mat) => {
-                if let Some(slot) = mphf.find(kmer) {
+                mat.row(mphf.index(kmer)).iter().map(|&b| b as u32).collect()
-                    mat.row(slot).iter().map(|&b| b as u32).collect()
-                } else {
-                    vec![0u32; n_genomes]
-                }
             }
             SrcLayerData::Count(mphf, mat) => {
-                if let Some(slot) = mphf.find(kmer) {
+                mat.row(mphf.index(kmer)).iter().copied().collect()
-                    mat.row(slot).iter().copied().collect()
-                } else {
-                    vec![0u32; n_genomes]
-                }
             }
         }
     }
@@ -161,6 +155,7 @@ impl KmerPartition {
         mode: MergeMode,
         n_dst_genomes: usize,
         block_bits: u8,
+        evidence: &IndexMode,
     ) -> SKResult<()> {
         let dst_index_dir = self.part_dir(i).join(INDEX_SUBDIR);
         if !dst_index_dir.exists() {
@@ -208,7 +203,7 @@ impl KmerPartition {
         let new_layer_idx = n_dst_layers;
         let new_layer_dir = dst_index_dir.join(format!("layer_{new_layer_idx}"));
 
-        if any_new {
+        let n_new = if any_new {
             g.compute_degrees();
             fs::create_dir_all(&new_layer_dir)?;
             let mut uw = Layer::<()>::unitig_writer(&new_layer_dir).map_err(olm_to_sk)?;
@@ -216,16 +211,18 @@ impl KmerPartition {
                 uw.write(&unitig)?;
             }
             uw.close()?;
-            Layer::<()>::build(&new_layer_dir, block_bits, &IndexMode::Exact).map_err(olm_to_sk)?;
+            Layer::<()>::build(&new_layer_dir, block_bits, evidence).map_err(olm_to_sk)?;
-        }
+            g.len()
+        } else {
+            0
+        };
         drop(g);
 
         let new_mphf = if any_new {
-            Some(MphfLayer::open(&new_layer_dir, &IndexMode::Exact).map_err(olm_to_sk)?)
+            Some(MphfOnly::open(&new_layer_dir).map_err(olm_to_sk)?)
         } else {
             None
         };
-        let n_new = new_mphf.as_ref().map_or(0, |m| m.n());
 
         // ── Prepare matrix directories for the new layer ──────────────────────
         // Absent columns (dst genomes) are written via append_column (all-zero/false).
@@ -303,7 +300,7 @@ 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, &src_meta.mode)?;
+                let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
 
                 for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                     let values = src_data.lookup(kmer, *src_n);
@@ -312,13 +309,12 @@ impl KmerPartition {
                         if let Some((dst_layer, hit)) = dst_map.query(kmer) {
                             exist_builders[dst_layer][builder_idx].set_val(hit.slot, value);
                         } else if let Some(ref mphf) = new_mphf {
-                            if let Some(slot) = mphf.find(kmer) {
+                            let slot = mphf.index(kmer);
                             new_src_builders[builder_idx].set_val(slot, value);
                         }
                     }
                 }
             }
-            }
             col_offset += src_n;
         }
 

src/obikpartitionner/src/rebuild_layer.rs

@@ -117,7 +117,7 @@ impl KmerPartition {
             if !unitigs_path.exists() { continue; }
 
             let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
-            let src_data = SrcLayerData::open(&src_layer_dir, mode, &src_meta.mode)?;
+            let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
 
             for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                 let row = src_data.lookup(kmer, n_genomes);
@@ -182,7 +182,7 @@ impl KmerPartition {
             if !unitigs_path.exists() { continue; }
 
             let reader = UnitigFileReader::open_sequential(&unitigs_path)?;
-            let src_data = SrcLayerData::open(&src_layer_dir, mode, &src_meta.mode)?;
+            let src_data = SrcLayerData::open(&src_layer_dir, mode)?;
 
             for (kmer, _, _) in reader.iter_indexed_canonical_kmers() {
                 let row = src_data.lookup(kmer, n_genomes);

src/obikseq/src/kmer.rs

@@ -1,7 +1,8 @@
-//! Compact 2-bit kmer stored as a left-aligned u64.
+//! Compact 2-bit kmer stored as a left-aligned [`RawKmer`].
 //!
-//! Nucleotide 0 occupies bits 63–62, nucleotide i occupies bits 63−2i and 62−2i.
+//! Nucleotide 0 occupies bits KMER_BITS−1 and KMER_BITS−2, nucleotide i occupies
-//! The low 64−2·len bits are always zero.
+//! bits KMER_BITS−1−2i and KMER_BITS−2−2i.
+//! The low `KMER_BITS − 2·len` bits are always zero.
 //!
 //! The length is not stored in the struct — it is supplied by the [`KmerLength`]
 //! type parameter.  Two public marker types cover the common cases:
@@ -15,6 +16,17 @@
 //! Tests that need a fixed length independent of the global singletons can use
 //! [`ConstLen<N>`].
 
+/// Underlying storage type for a raw (2-bit-per-base, left-aligned) kmer.
+///
+/// All kmer bit-width constants (`KMER_BITS`) and shift calculations are derived
+/// from this type. To extend the maximum supported k beyond 32, change this alias
+/// to `u128` and update `KMER_BITS` — callers that use `RawKmer` directly will
+/// then pick up the wider type automatically.
+pub type RawKmer = u64;
+
+/// Bit width of [`RawKmer`]: the number of bits available for nucleotide encoding.
+pub const KMER_BITS: usize = 64;
+
 use serde::Serialize;
 use std::io::{self, Write};
 use std::marker::PhantomData;
@@ -109,35 +121,35 @@ impl Annotation for KmerAnnotation {}
 
 // ── KmerOf ────────────────────────────────────────────────────────────────────
 
-/// A DNA kmer of length `L::len()` encoded as a left-aligned u64 (2 bits/nucleotide, MSB-first).
+/// A DNA kmer of length `L::len()` encoded as a left-aligned [`RawKmer`] (2 bits/nucleotide, MSB-first).
-/// The low `64 − 2·L::len()` bits are always zero.
+/// The low `KMER_BITS − 2·L::len()` bits are always zero.
 #[repr(transparent)]
 #[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
-pub struct KmerOf<L: KmerLength>(u64, PhantomData<L>);
+pub struct KmerOf<L: KmerLength>(RawKmer, PhantomData<L>);
 
 impl<L: KmerLength> KmerOf<L> {
-    /// Wrap a raw left-aligned u64 value as a kmer.
+    /// Wrap a raw left-aligned [`RawKmer`] value as a kmer.
     #[inline]
-    pub const fn from_raw(raw: u64) -> Self {
+    pub const fn from_raw(raw: RawKmer) -> Self {
         KmerOf(raw, PhantomData)
     }
 
-    /// Wrap a raw right-aligned u64 value, shifting it into left-aligned position.
+    /// Wrap a raw right-aligned [`RawKmer`] value, shifting it into left-aligned position.
     #[inline]
-    pub fn from_raw_right(raw: u64) -> Self {
+    pub fn from_raw_right(raw: RawKmer) -> Self {
-        KmerOf(raw << (64 - 2 * L::len()), PhantomData)
+        KmerOf(raw << (KMER_BITS - 2 * L::len()), PhantomData)
     }
 
-    /// Return the raw left-aligned u64 value.
+    /// Return the raw left-aligned [`RawKmer`] value.
     #[inline]
-    pub fn raw(&self) -> u64 {
+    pub fn raw(&self) -> RawKmer {
         self.0
     }
 
-    /// Return the raw right-aligned u64 value.
+    /// Return the raw right-aligned [`RawKmer`] value.
     #[inline]
-    pub fn raw_right(&self) -> u64 {
+    pub fn raw_right(&self) -> RawKmer {
-        self.0 >> (64 - 2 * L::len())
+        self.0 >> (KMER_BITS - 2 * L::len())
     }
 
     /// Encode the first `L::len()` nucleotides of an ASCII slice into a kmer.
@@ -153,11 +165,11 @@ impl<L: KmerLength> KmerOf<L> {
                 seql: ascii.len(),
             });
         }
-        let mut val = 0u64;
+        let mut val: RawKmer = 0;
         for i in 0..k {
-            val = (val << 2) | encode_base(ascii[i]) as u64;
+            val = (val << 2) | encode_base(ascii[i]) as RawKmer;
         }
-        Ok(KmerOf(val << (64 - 2 * k), PhantomData))
+        Ok(KmerOf(val << (KMER_BITS - 2 * k), PhantomData))
     }
 
     /// Decode into a freshly allocated ASCII `Vec<u8>`.
@@ -193,27 +205,27 @@ impl<L: KmerLength> KmerOf<L> {
         let x = x.swap_bytes();
         let x = ((x >> 4) & 0x0F0F0F0F0F0F0F0F) | ((x & 0x0F0F0F0F0F0F0F0F) << 4);
         let x = ((x >> 2) & 0x3333333333333333) | ((x & 0x3333333333333333) << 2);
-        KmerOf(x << (64 - 2 * k), PhantomData)
+        KmerOf(x << (KMER_BITS - 2 * k), PhantomData)
     }
 
     /// Slide the window one base to the right: drop nucleotide 0, append `nuc` at position `L::len()-1`.
     pub fn push_right(self, nuc: u8) -> Self {
         let k = L::len();
-        let shifted = self.0 << 2 & (!0u64 << (64 - 2 * (k - 1)));
+        let shifted = self.0 << 2 & (RawKmer::MAX << (KMER_BITS - 2 * (k - 1)));
-        KmerOf(shifted | ((nuc as u64 & 3) << (64 - 2 * k)), PhantomData)
+        KmerOf(shifted | ((nuc as RawKmer & 3) << (KMER_BITS - 2 * k)), PhantomData)
     }
 
     /// Slide the window one base to the left: drop nucleotide `L::len()-1`, prepend `nuc` at position 0.
     pub fn push_left(self, nuc: u8) -> Self {
         let k = L::len();
-        let shifted = (self.0 >> 2) & (!0u64 << (64 - 2 * k));
+        let shifted = (self.0 >> 2) & (RawKmer::MAX << (KMER_BITS - 2 * k));
-        KmerOf(shifted | ((nuc as u64 & 3) << 62), PhantomData)
+        KmerOf(shifted | ((nuc as RawKmer & 3) << (KMER_BITS - 2)), PhantomData)
     }
 
     /// Returns `true` if the last `L::len()-1` nucleotides of `self` equal the first `L::len()-1` of `other`.
     pub fn is_overlapping(self, other: Self) -> bool {
         let k = L::len();
-        let mask = !0u64 << (64 - 2 * (k - 1));
+        let mask = RawKmer::MAX << (KMER_BITS - 2 * (k - 1));
         (self.0 << 2 & mask) == (other.0 & mask)
     }
 }
@@ -231,7 +243,7 @@ impl<L: KmerLength> Sequence for KmerOf<L> {
 
     #[inline]
     fn nucleotide(&self, i: usize) -> u8 {
-        ((self.0 >> (62 - 2 * i)) & 0b11) as u8
+        ((self.0 >> (KMER_BITS - 2 - 2 * i)) & 0b11) as u8
     }
 
     #[inline]
@@ -255,21 +267,21 @@ impl<L: KmerLength> Sequence for KmerOf<L> {
 /// [`CanonicalKmerOf::from_raw_unchecked`] (trusted paths such as deserialisation).
 #[repr(transparent)]
 #[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
-pub struct CanonicalKmerOf<L: KmerLength>(u64, PhantomData<L>);
+pub struct CanonicalKmerOf<L: KmerLength>(RawKmer, PhantomData<L>);
 
 impl<L: KmerLength> CanonicalKmerOf<L> {
-    /// Wrap a raw left-aligned u64 without verifying the canonical invariant.
+    /// Wrap a raw left-aligned [`RawKmer`] without verifying the canonical invariant.
     ///
     /// # Safety (logical)
     /// The caller must guarantee `raw == min(raw, revcomp(raw))`.
     #[inline]
-    pub fn from_raw_unchecked(raw: u64) -> Self {
+    pub fn from_raw_unchecked(raw: RawKmer) -> Self {
         CanonicalKmerOf(raw, PhantomData)
     }
 
-    /// Return the raw left-aligned u64 value.
+    /// Return the raw left-aligned [`RawKmer`] value.
     #[inline]
-    pub fn raw(&self) -> u64 {
+    pub fn raw(&self) -> RawKmer {
         self.0
     }
 
@@ -307,25 +319,25 @@ impl<L: KmerLength> CanonicalKmerOf<L> {
     /// Return the four left canonical neighbours (each already canonical).
     pub fn left_canonical_neighbors(&self) -> [CanonicalKmerOf<L>; 4] {
         let k = L::len();
-        let shifted = (self.0 >> 2) & (!0u64 << (64 - 2 * k));
+        let shifted = (self.0 >> 2) & (RawKmer::MAX << (KMER_BITS - 2 * k));
         [
             KmerOf::<L>(shifted, PhantomData).canonical(),
-            KmerOf::<L>(shifted | (1u64 << 62), PhantomData).canonical(),
+            KmerOf::<L>(shifted | ((1 as RawKmer) << (KMER_BITS - 2)), PhantomData).canonical(),
-            KmerOf::<L>(shifted | (2u64 << 62), PhantomData).canonical(),
+            KmerOf::<L>(shifted | ((2 as RawKmer) << (KMER_BITS - 2)), PhantomData).canonical(),
-            KmerOf::<L>(shifted | (3u64 << 62), PhantomData).canonical(),
+            KmerOf::<L>(shifted | ((3 as RawKmer) << (KMER_BITS - 2)), PhantomData).canonical(),
         ]
     }
 
     /// Return the four right canonical neighbours (each already canonical).
     pub fn right_canonical_neighbors(&self) -> [CanonicalKmerOf<L>; 4] {
         let k = L::len();
-        let shifted = self.0 << 2 & (!0u64 << (64 - 2 * (k - 1)));
+        let shifted = self.0 << 2 & (RawKmer::MAX << (KMER_BITS - 2 * (k - 1)));
-        let shift = 64 - 2 * k;
+        let shift = KMER_BITS - 2 * k;
         [
             KmerOf::<L>(shifted, PhantomData).canonical(),
-            KmerOf::<L>(shifted | (1u64 << shift), PhantomData).canonical(),
+            KmerOf::<L>(shifted | ((1 as RawKmer) << shift), PhantomData).canonical(),
-            KmerOf::<L>(shifted | (2u64 << shift), PhantomData).canonical(),
+            KmerOf::<L>(shifted | ((2 as RawKmer) << shift), PhantomData).canonical(),
-            KmerOf::<L>(shifted | (3u64 << shift), PhantomData).canonical(),
+            KmerOf::<L>(shifted | ((3 as RawKmer) << shift), PhantomData).canonical(),
         ]
     }
 
@@ -349,7 +361,7 @@ impl<L: KmerLength> Sequence for CanonicalKmerOf<L> {
 
     #[inline]
     fn nucleotide(&self, i: usize) -> u8 {
-        ((self.0 >> (62 - 2 * i)) & 0b11) as u8
+        ((self.0 >> (KMER_BITS - 2 - 2 * i)) & 0b11) as u8
     }
 
     fn canonical(&self) -> Self::Canonical {
@@ -386,7 +398,7 @@ pub type Minimizer = CanonicalKmerOf<MLen>;
 /// 64-bit representation directly, which is useful when the canonical
 /// invariant is not required or has already been handled.
 #[inline]
-pub fn hash_kmer(raw: u64) -> u64 {
+pub fn hash_kmer(raw: RawKmer) -> u64 {
     mix64(raw ^ 0x9e3779b97f4a7c15)
 }
 

src/obikseq/src/lib.rs

@@ -20,7 +20,7 @@ pub mod superkmer;
 pub mod unitig;
 
 pub use annotations::Annotation;
-pub use kmer::{CanonicalKmer, Kmer, Minimizer, hash_kmer};
+pub use kmer::{CanonicalKmer, Kmer, Minimizer, RawKmer, KMER_BITS, hash_kmer};
 pub use packed_seq::MAX_KMERS_PER_CHUNK;
 pub use params::{k, m, set_k, set_m};
 pub use routable::RoutableSuperKmer;

src/obikseq/src/packed_seq.rs

@@ -18,7 +18,7 @@ use bitvec::prelude::*;
 
 use crate::Sequence;
 use crate::encoding::{DEC4, encode_base};
-use crate::kmer::{CanonicalKmer, Kmer, KmerError, KLen, KmerLength, KmerOf, MLen, Minimizer};
+use crate::kmer::{CanonicalKmer, Kmer, KmerError, KLen, KmerLength, KmerOf, MLen, Minimizer, RawKmer, KMER_BITS};
 use crate::params::k;
 use crate::revcomp_lookup::REVCOMP4;
 
@@ -198,8 +198,8 @@ impl PackedSeq {
             return Err(KmerError::OutOfBounds { position: i, k: len, seql });
         }
         let bits = self.seq.view_bits::<Msb0>();
-        let raw: u64 = bits[i * 2..(i + len) * 2].load_be();
+        let raw: RawKmer = bits[i * 2..(i + len) * 2].load_be();
-        Ok(KmerOf::from_raw(raw << (64 - 2 * len)))
+        Ok(KmerOf::from_raw(raw << (KMER_BITS - 2 * len)))
     }
 
     /// Extract the kmer of length `params::k()` at nucleotide position `i`. Zero allocation.
@@ -322,9 +322,9 @@ impl AsRef<PackedSeq> for PackedSeq {
 /// sequence into the iterator, so no reference escapes the closure.
 pub struct PackedSeqKmerIter<S> {
     seq: S,
-    mask: u64,
+    mask: RawKmer,
     lshift: usize,
-    current: u64,
+    current: RawKmer,
     pos: usize,
     max_pos: usize,
 }
@@ -341,8 +341,8 @@ impl<S: AsRef<PackedSeq>> PackedSeqKmerIter<S> {
         let ps = seq.as_ref();
         let seql = ps.seql();
         let klen = k();
-        let lshift = 64 - klen * 2;
+        let lshift = KMER_BITS - klen * 2;
-        let mask = ((!0u128) << (lshift + 2)) as u64;
+        let mask = ((!0u128) << (lshift + 2)) as RawKmer;
         let current = if seql >= klen {
             ps.extract::<KLen>(0).map(|km| km.raw()).unwrap_or(0)
         } else {
@@ -362,7 +362,7 @@ impl<S: AsRef<PackedSeq>> Iterator for PackedSeqKmerIter<S> {
         let result = Kmer::from_raw(self.current);
         if self.pos < self.max_pos {
             let inner_shift = 6 - 2 * (self.pos & 3);
-            let nuc = ((self.seq.as_ref().seq[self.pos / 4] >> inner_shift) & 3) as u64;
+            let nuc = ((self.seq.as_ref().seq[self.pos / 4] >> inner_shift) & 3) as RawKmer;
             self.current = ((self.current << 2) & self.mask) | (nuc << self.lshift);
         }
         self.pos += 1;

src/obilayeredmap/src/lib.rs

@@ -12,4 +12,4 @@ pub use layer::{Hit, Layer, LayerData};
 pub use layered_store::LayeredStore;
 pub use map::LayeredMap;
 pub use meta::{IndexMode, PartitionMeta};
-pub use mphf_layer::MphfLayer;
+pub use mphf_layer::{MphfLayer, MphfOnly};

src/obilayeredmap/src/mphf_layer.rs

@@ -118,7 +118,7 @@ impl MphfLayer {
             }
             LayerEvidence::Approx { unitigs_path, .. } => {
                 let reader = UnitigFileReader::open_sequential(unitigs_path).ok()?;
-                for stored in reader.iter_canonical_kmers() {
+                for (stored, _, _) in reader.iter_indexed_canonical_kmers() {
                     if self.mphf.index(&stored.raw()) == slot {
                         return if stored == kmer { Some(slot) } else { None };
                     }
@@ -129,7 +129,31 @@ impl MphfLayer {
     }
 
     pub fn n(&self) -> usize { self.n }
+}
 
+// ── MphfOnly ──────────────────────────────────────────────────────────────────
+
+/// Lightweight wrapper that loads only the MPHF file, without evidence or unitigs.
+///
+/// Use this when the caller guarantees that all queried kmers are in the MPHF
+/// domain (e.g. when iterating the source's own unitigs during merge).
+pub struct MphfOnly(Mphf);
+
+impl MphfOnly {
+    pub fn open(dir: &Path) -> OLMResult<Self> {
+        let mphf: Mphf = Mphf::load_full(&dir.join(MPHF_FILE))
+            .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
+        Ok(Self(mphf))
+    }
+
+    /// Return the slot for `kmer`. Only valid when `kmer` is in the MPHF domain.
+    #[inline]
+    pub fn index(&self, kmer: CanonicalKmer) -> usize {
+        self.0.index(&kmer.raw())
+    }
+}
+
+impl MphfLayer {
     // ── Build helpers ─────────────────────────────────────────────────────────
 
     pub fn unitig_writer(dir: &Path) -> OLMResult<UnitigFileWriter> {
@@ -196,7 +220,7 @@ impl MphfLayer {
 
         let mut fw = FingerprintVecWriter::new(n, b);
 
-        for kmer in unitigs.iter_canonical_kmers() {
+        for (kmer, _, _) in unitigs.iter_indexed_canonical_kmers() {
             let slot = mphf.index(&kmer.raw());
             if slot >= n {
                 return Err(OLMError::Mphf("slot out of bounds".into()));
@@ -281,7 +305,7 @@ impl MphfLayer {
 
             IndexMode::Approx { b, .. } => {
                 let mut fw = FingerprintVecWriter::new(n, *b);
-                for kmer in unitigs2.iter_canonical_kmers() {
+                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);

src/obilayeredmap/src/tests/layer.rs

@@ -2,7 +2,7 @@ use super::*;
 use obicompactvec::PersistentCompactIntMatrix;
 use obikseq::{set_k, Kmer, Sequence as _, Unitig};
 use obiskio::DEFAULT_BLOCK_BITS;
-use crate::meta::EvidenceKind;
+use crate::meta::IndexMode;
 use tempfile::tempdir;
 
 fn write_unitigs(dir: &Path, seqs: &[&[u8]]) {
@@ -15,7 +15,8 @@ fn write_unitigs(dir: &Path, seqs: &[&[u8]]) {
 
 fn all_canonical_kmers(dir: &Path) -> Vec<CanonicalKmer> {
     UnitigFileReader::open_sequential(&dir.join(UNITIGS_FILE)).unwrap()
-        .iter_canonical_kmers()
+        .iter_indexed_canonical_kmers()
+        .map(|(kmer, _, _)| kmer)
         .collect()
 }
 
@@ -25,8 +26,8 @@ fn build_and_query_all_kmers_found() {
     let dir = tempdir().unwrap();
     write_unitigs(dir.path(), &[b"AAAACGT"]);
     let kmers = all_canonical_kmers(dir.path());
-    Layer::<()>::build(dir.path(), DEFAULT_BLOCK_BITS, &EvidenceKind::Exact).unwrap();
+    Layer::<()>::build(dir.path(), DEFAULT_BLOCK_BITS, &IndexMode::Exact).unwrap();
-    let layer = Layer::<()>::open(dir.path()).unwrap();
+    let layer = Layer::<()>::open(dir.path(), &IndexMode::Exact).unwrap();
     for kmer in kmers {
         assert!(layer.query(kmer).is_some(), "kmer should be present");
     }
@@ -43,10 +44,10 @@ fn counts_are_stored_and_retrieved() {
     Layer::<PersistentCompactIntMatrix>::build(
         dir.path(),
         DEFAULT_BLOCK_BITS,
-        &EvidenceKind::Exact,
+        &IndexMode::Exact,
         |kmer| count_map.get(&kmer).copied().unwrap_or(0),
     ).unwrap();
-    let layer = Layer::<PersistentCompactIntMatrix>::open(dir.path()).unwrap();
+    let layer = Layer::<PersistentCompactIntMatrix>::open(dir.path(), &IndexMode::Exact).unwrap();
     for kmer in &kmers {
         let hit = layer.query(*kmer).expect("kmer must be present");
         assert_eq!(hit.data[0], count_map[kmer]);
@@ -58,8 +59,8 @@ fn query_absent_returns_none() {
     set_k(4);
     let dir = tempdir().unwrap();
     write_unitigs(dir.path(), &[b"AAAACGT"]);
-    Layer::<()>::build(dir.path(), DEFAULT_BLOCK_BITS, &EvidenceKind::Exact).unwrap();
+    Layer::<()>::build(dir.path(), DEFAULT_BLOCK_BITS, &IndexMode::Exact).unwrap();
-    let layer = Layer::<()>::open(dir.path()).unwrap();
+    let layer = Layer::<()>::open(dir.path(), &IndexMode::Exact).unwrap();
     let absent = Kmer::from_ascii(b"CCCC").unwrap().canonical();
     assert!(layer.query(absent).is_none());
 }
@@ -69,9 +70,9 @@ fn open_after_build_is_consistent() {
     set_k(4);
     let dir = tempdir().unwrap();
     write_unitigs(dir.path(), &[b"AAAACGT"]);
-    let n = Layer::<PersistentCompactIntMatrix>::build(dir.path(), DEFAULT_BLOCK_BITS, &EvidenceKind::Exact, |_| 7).unwrap();
+    let n = Layer::<PersistentCompactIntMatrix>::build(dir.path(), DEFAULT_BLOCK_BITS, &IndexMode::Exact, |_| 7).unwrap();
     assert_eq!(n, 4);
-    let layer = Layer::<PersistentCompactIntMatrix>::open(dir.path()).unwrap();
+    let layer = Layer::<PersistentCompactIntMatrix>::open(dir.path(), &IndexMode::Exact).unwrap();
     let kmer = Kmer::from_ascii(b"AAAA").unwrap().canonical();
     let hit = layer.query(kmer).expect("AAAA must be present");
     assert_eq!(hit.data[0], 7);

src/obilayeredmap/src/tests/map.rs

@@ -1,6 +1,7 @@
 use super::*;
 use obicompactvec::PersistentCompactIntMatrix;
 use obikseq::{set_k, Sequence as _, Unitig};
+use crate::meta::IndexMode;
 use tempfile::tempdir;
 
 fn push_unitigs_and_layer(
@@ -24,7 +25,7 @@ fn canonical(ascii: &[u8]) -> CanonicalKmer {
 fn create_empty_map() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let map = LayeredMap::<()>::create(dir.path()).unwrap();
+    let map = LayeredMap::<()>::create(dir.path(), IndexMode::Exact).unwrap();
     assert_eq!(map.n_layers(), 0);
 }
 
@@ -33,7 +34,7 @@ fn open_reloads_layer_count() {
     set_k(4);
     let dir = tempdir().unwrap();
     {
-        let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path()).unwrap();
+        let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path(), IndexMode::Exact).unwrap();
         push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
     }
     let map = LayeredMap::<PersistentCompactIntMatrix>::open(dir.path()).unwrap();
@@ -44,7 +45,7 @@ fn open_reloads_layer_count() {
 fn query_finds_kmer_in_layer_zero() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path()).unwrap();
+    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path(), IndexMode::Exact).unwrap();
     push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 3);
     let kmer = canonical(b"AAAC");
     let (layer_idx, hit) = map.query(kmer).expect("kmer must be found");
@@ -56,7 +57,7 @@ fn query_finds_kmer_in_layer_zero() {
 fn query_finds_kmer_in_correct_layer() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path()).unwrap();
+    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path(), IndexMode::Exact).unwrap();
     push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
     push_unitigs_and_layer(&mut map, &[b"GGGACGT"], 2);
     assert_eq!(map.n_layers(), 2);
@@ -74,7 +75,7 @@ fn query_finds_kmer_in_correct_layer() {
 fn query_absent_returns_none() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path()).unwrap();
+    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path(), IndexMode::Exact).unwrap();
     push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
     let absent = canonical(b"CCCC");
     assert!(map.query(absent).is_none());
@@ -84,7 +85,7 @@ fn query_absent_returns_none() {
 fn push_layer_from_map_convenience() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path()).unwrap();
+    let mut map = LayeredMap::<PersistentCompactIntMatrix>::create(dir.path(), IndexMode::Exact).unwrap();
     let mut w = map.next_layer_writer().unwrap();
     w.write(&Unitig::from_ascii(b"AAAACGT")).unwrap();
     w.close().unwrap();

src/obiskio/src/tests/unitig_index.rs

@@ -181,30 +181,6 @@ fn iter_kmers_two_chunks_order() {
     }
 }
 
-// ── iter_canonical_kmers ──────────────────────────────────────────────────────
-
-#[test]
-fn iter_canonical_kmers_all_canonical() {
-    set_k(4);
-    let (_dir, r) = write_read(&[b"AAAACG", b"CCCCAG"]);
-    for kmer in r.iter_canonical_kmers() {
-        // canonical of a canonical kmer is itself
-        assert_eq!(kmer.raw(), kmer.canonical().raw());
-    }
-}
-
-#[test]
-fn iter_canonical_kmers_matches_iter_kmers() {
-    set_k(4);
-    let (_dir, r) = write_read(&[b"AAAACG", b"CCCCAG"]);
-    let canonical: Vec<CanonicalKmer> = r.iter_canonical_kmers().collect();
-    let raw: Vec<Kmer> = r.iter_kmers().collect();
-    assert_eq!(canonical.len(), raw.len());
-    for (ck, rk) in canonical.iter().zip(raw.iter()) {
-        assert_eq!(ck.raw(), rk.canonical().raw());
-    }
-}
-
 // ── iter_indexed_canonical_kmers ──────────────────────────────────────────────
 
 #[test]

src/obiskio/src/unitig_index.rs

@@ -370,11 +370,6 @@ impl UnitigFileReader {
             .flat_map(|(_, u)| u.into_kmers())
     }
 
-    pub fn iter_canonical_kmers(&self) -> impl Iterator<Item = CanonicalKmer> + '_ {
-        self.iter_chunks_sequential()
-            .flat_map(|(_, u)| u.into_canonical_kmers())
-    }
-
     pub fn iter_indexed_canonical_kmers(
         &self,
     ) -> impl Iterator<Item = (CanonicalKmer, usize, usize)> + '_ {