refactor(obilayeredmap): support generic payload types

Replace the hardcoded `Counts` module with a generic `LayerData` trait, parameterizing `Layer` and `LayeredMap` over arbitrary payload types. This decouples read-path access from build-path logic, enabling both set membership and count-based indexing via `PersistentCompactIntVec`. Adds the `obicompactvec` dependency, implements streaming layer construction, and expands test coverage for persistence and multi-layer resolution.

src/obilayeredmap/Cargo.toml

@@ -4,8 +4,9 @@ version = "0.1.0"
 edition = "2024"
 
 [dependencies]
-obikseq      = { path = "../obikseq" }
-obiskio      = { path = "../obiskio" }
+obikseq        = { path = "../obikseq" }
+obiskio        = { path = "../obiskio" }
+obicompactvec  = { path = "../obicompactvec" }
 ptr_hash     = "1.1"
 cacheline-ef = "1.1"
 epserde      = "0.8"

src/obilayeredmap/src/counts.rs

@@ -1,54 +0,0 @@
-// u32 per MPHF slot: raw occurrence count for the kmer at that slot.
-
-use std::fs::File;
-use std::io::{BufWriter, Write};
-use std::path::Path;
-
-use memmap2::Mmap;
-
-use crate::error::{OLMError, OLMResult};
-
-pub struct Counts {
-    mmap: Mmap,
-}
-
-impl Counts {
-    pub fn open(path: &Path) -> OLMResult<Self> {
-        let f = File::open(path)?;
-        let mmap = unsafe { Mmap::map(&f)? };
-        Ok(Self { mmap })
-    }
-
-    #[inline]
-    pub fn get(&self, slot: usize) -> u32 {
-        let off = slot * 4;
-        u32::from_le_bytes(self.mmap[off..off + 4].try_into().unwrap())
-    }
-
-    pub fn len(&self) -> usize {
-        self.mmap.len() / 4
-    }
-}
-
-pub struct CountsWriter {
-    buf: Vec<u32>,
-}
-
-impl CountsWriter {
-    pub fn new(n_slots: usize) -> Self {
-        Self { buf: vec![0u32; n_slots] }
-    }
-
-    #[inline]
-    pub fn set(&mut self, slot: usize, count: u32) {
-        self.buf[slot] = count;
-    }
-
-    pub fn write(self, path: &Path) -> OLMResult<()> {
-        let mut f = BufWriter::new(File::create(path)?);
-        for v in self.buf {
-            f.write_all(&v.to_le_bytes()).map_err(OLMError::Io)?;
-        }
-        Ok(())
-    }
-}

src/obilayeredmap/src/layer.rs

@@ -4,130 +4,185 @@ use std::path::Path;
 
 use cacheline_ef::{CachelineEf, CachelineEfVec};
 use epserde::prelude::*;
+use obicompactvec::{PersistentCompactIntVec, PersistentCompactIntVecBuilder};
 use obikseq::CanonicalKmer;
 use obiskio::{UnitigFileReader, UnitigFileWriter};
 use ptr_hash::{PtrHash, PtrHashParams, bucket_fn::CubicEps, hash::Xx64};
 
-use crate::counts::{Counts, CountsWriter};
 use crate::error::{OLMError, OLMResult};
 use crate::evidence::{Evidence, EvidenceWriter};
 
-const MPHF_FILE: &str = "mphf.bin";
-const UNITIGS_FILE: &str = "unitigs.bin";
+pub(crate) const MPHF_FILE:    &str = "mphf.bin";
+pub(crate) const UNITIGS_FILE: &str = "unitigs.bin";
 const EVIDENCE_FILE: &str = "evidence.bin";
-const COUNTS_FILE: &str = "counts.bin";
+const COUNTS_FILE:   &str = "counts.pciv";
 
 type Mphf = PtrHash<u64, CubicEps, CachelineEfVec<Vec<CachelineEf>>, Xx64, Vec<u8>>;
 
-pub struct Layer {
-    mphf: Mphf,
+// ── Trait ─────────────────────────────────────────────────────────────────────
+
+pub trait LayerData: Sized {
+    type Item;
+    fn open(layer_dir: &Path) -> OLMResult<Self>;
+    fn read(&self, slot: usize) -> Self::Item;
+}
+
+impl LayerData for () {
+    type Item = ();
+    fn open(_layer_dir: &Path) -> OLMResult<Self> { Ok(()) }
+    fn read(&self, _slot: usize) {}
+}
+
+impl LayerData for PersistentCompactIntVec {
+    type Item = u32;
+    fn open(layer_dir: &Path) -> OLMResult<Self> {
+        PersistentCompactIntVec::open(&layer_dir.join(COUNTS_FILE)).map_err(OLMError::Io)
+    }
+    fn read(&self, slot: usize) -> u32 { self.get(slot) }
+}
+
+// ── Structures ────────────────────────────────────────────────────────────────
+
+pub struct Layer<D: LayerData = ()> {
+    mphf:     Mphf,
     evidence: Evidence,
-    unitigs: UnitigFileReader,
-    counts: Counts,
+    unitigs:  UnitigFileReader,
+    data:     D,
 }
 
-pub struct Hit {
+pub struct Hit<T = ()> {
     pub slot: usize,
-    pub count: u32,
+    pub data: T,
 }
 
-impl Layer {
+// ── Common read path ──────────────────────────────────────────────────────────
+
+impl<D: LayerData> Layer<D> {
     pub fn open(path: &Path) -> OLMResult<Self> {
         let mphf: Mphf = Mphf::load_full(&path.join(MPHF_FILE))
             .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
-
-        let unitigs = UnitigFileReader::open(&path.join(UNITIGS_FILE))?;
+        let unitigs  = UnitigFileReader::open(&path.join(UNITIGS_FILE))?;
         let evidence = Evidence::open(&path.join(EVIDENCE_FILE))?;
-        let counts = Counts::open(&path.join(COUNTS_FILE))?;
-
-        Ok(Self { mphf, evidence, unitigs, counts })
+        let data     = D::open(path)?;
+        Ok(Self { mphf, evidence, unitigs, data })
     }
 
-    pub fn query(&self, kmer: CanonicalKmer) -> Option<Hit> {
+    pub fn query(&self, kmer: CanonicalKmer) -> Option<Hit<D::Item>> {
         let slot = self.mphf.index(&kmer.raw());
         let (chunk_id, rank) = self.evidence.decode(slot);
-        if self
-            .unitigs
-            .verify_canonical_kmer(chunk_id as usize, rank as usize, kmer)
-        {
-            Some(Hit { slot, count: self.counts.get(slot) })
+        if self.unitigs.verify_canonical_kmer(chunk_id as usize, rank as usize, kmer) {
+            Some(Hit { slot, data: self.data.read(slot) })
         } else {
             None
         }
     }
 
-    /// Build a layer from unitigs already written to `out_dir/unitigs.bin`.
-    ///
-    /// `count_of` maps each canonical kmer to its occurrence count.
-    /// Returns the number of kmers indexed.
-    pub fn build(out_dir: &Path, count_of: impl Fn(CanonicalKmer) -> u32) -> OLMResult<usize> {
-        use rayon::prelude::*;
-
-        let unitigs = UnitigFileReader::open(&out_dir.join(UNITIGS_FILE))?;
-        let n = unitigs.n_kmers();
-
-        if n == 0 {
-            fs::File::create(out_dir.join(EVIDENCE_FILE))?;
-            fs::File::create(out_dir.join(COUNTS_FILE))?;
-            let mphf: Mphf = Mphf::try_new(&[] as &[u64], PtrHashParams::<CubicEps>::default())
-                .ok_or_else(|| OLMError::Mphf("construction failed".into()))?;
-            mphf.store(&out_dir.join(MPHF_FILE))
-                .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
-            return Ok(0);
-        }
-
-        // First pass: build the MPHF from a cloneable parallel iterator.
-        // flat_map_iter: outer chunks in parallel, inner kmer sliding-window sequential.
-        let keys = (0..unitigs.len())
-            .into_par_iter()
-            .flat_map_iter(|ci| unitigs.unitig(ci).into_canonical_kmers().map(|km| km.raw()));
-        let mphf: Mphf = Mphf::new_from_par_iter(n, keys, PtrHashParams::<CubicEps>::default());
-        mphf.store(&out_dir.join(MPHF_FILE))
-            .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
-
-        // Second pass: fill evidence and counts; verify MPHF correctness inline.
-        // seen is a compact bitset (n/8 bytes) — no extra iteration needed.
-        let mut ev   = EvidenceWriter::new(n);
-        let mut cnt  = CountsWriter::new(n);
-        let mut seen = vec![0u8; (n + 7) / 8];
-
-        for (kmer, chunk_id, rank) in unitigs.iter_indexed_canonical_kmers() {
-            let slot = mphf.index(&kmer.raw());
-            if slot >= n {
-                return Err(OLMError::Mphf("MPHF construction failed: slot out of bounds".into()));
-            }
-            let byte = slot / 8;
-            let bit  = 1u8 << (slot % 8);
-            if seen[byte] & bit != 0 {
-                return Err(OLMError::Mphf("MPHF construction failed: duplicate slot".into()));
-            }
-            seen[byte] |= bit;
-            ev.set(slot, chunk_id as u32, rank as u8);
-            cnt.set(slot, count_of(kmer));
-        }
-
-        ev.write(&out_dir.join(EVIDENCE_FILE))?;
-        cnt.write(&out_dir.join(COUNTS_FILE))?;
-
-        Ok(n)
-    }
-
-    /// Convenience variant of `build` that accepts a `HashMap`.
-    pub fn build_from_map(
-        out_dir: &Path,
-        counts: &HashMap<CanonicalKmer, u32>,
-    ) -> OLMResult<usize> {
-        Self::build(out_dir, |kmer| counts.get(&kmer).copied().unwrap_or(0))
-    }
-
-    /// Return a `UnitigFileWriter` targeting this layer's `unitigs.bin`.
-    /// The caller writes unitigs, then calls `Layer::build` to finish the layer.
     pub fn unitig_writer(out_dir: &Path) -> OLMResult<UnitigFileWriter> {
         fs::create_dir_all(out_dir)?;
         Ok(UnitigFileWriter::create(&out_dir.join(UNITIGS_FILE))?)
     }
 }
 
+// ── Build helpers (private) ───────────────────────────────────────────────────
+
+fn build_mphf(out_dir: &Path, n: usize) -> OLMResult<Mphf> {
+    use rayon::prelude::*;
+    let unitigs = UnitigFileReader::open(&out_dir.join(UNITIGS_FILE))?;
+    let keys = (0..unitigs.len())
+        .into_par_iter()
+        .flat_map_iter(|ci| unitigs.unitig(ci).into_canonical_kmers().map(|km| km.raw()));
+    let mphf: Mphf = Mphf::new_from_par_iter(n, keys, PtrHashParams::<CubicEps>::default());
+    mphf.store(&out_dir.join(MPHF_FILE))
+        .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
+    Ok(mphf)
+}
+
+fn build_second_pass(
+    out_dir: &Path,
+    n: usize,
+    mphf: &Mphf,
+    fill_slot: &mut impl FnMut(usize, CanonicalKmer) -> OLMResult<()>,
+) -> OLMResult<()> {
+    let unitigs  = UnitigFileReader::open(&out_dir.join(UNITIGS_FILE))?;
+    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() {
+        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);
+        fill_slot(slot, kmer)?;
+    }
+
+    ev.write(&out_dir.join(EVIDENCE_FILE))?;
+    Ok(())
+}
+
+fn empty_layer(out_dir: &Path) -> OLMResult<()> {
+    fs::File::create(out_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(&out_dir.join(MPHF_FILE))
+        .map_err(|e| OLMError::InvalidLayer(e.to_string()))?;
+    Ok(())
+}
+
+// ── Mode 1 — set membership ───────────────────────────────────────────────────
+
+impl Layer<()> {
+    pub fn build(out_dir: &Path) -> OLMResult<usize> {
+        let unitigs = UnitigFileReader::open(&out_dir.join(UNITIGS_FILE))?;
+        let n = unitigs.n_kmers();
+        if n == 0 {
+            empty_layer(out_dir)?;
+            return Ok(0);
+        }
+        let mphf = build_mphf(out_dir, n)?;
+        build_second_pass(out_dir, n, &mphf, &mut |_, _| Ok(()))?;
+        Ok(n)
+    }
+}
+
+// ── Mode 2 — counts (PersistentCompactIntVec) ─────────────────────────────────
+
+impl Layer<PersistentCompactIntVec> {
+    pub fn build(out_dir: &Path, count_of: impl Fn(CanonicalKmer) -> u32) -> OLMResult<usize> {
+        let unitigs = UnitigFileReader::open(&out_dir.join(UNITIGS_FILE))?;
+        let n = unitigs.n_kmers();
+        if n == 0 {
+            empty_layer(out_dir)?;
+            PersistentCompactIntVecBuilder::new(0, &out_dir.join(COUNTS_FILE))
+                .and_then(|b| b.close())
+                .map_err(OLMError::Io)?;
+            return Ok(0);
+        }
+        let mphf = build_mphf(out_dir, n)?;
+        let mut cnt = PersistentCompactIntVecBuilder::new(n, &out_dir.join(COUNTS_FILE))
+            .map_err(OLMError::Io)?;
+        build_second_pass(out_dir, n, &mphf, &mut |slot, kmer| {
+            cnt.set(slot, count_of(kmer));
+            Ok(())
+        })?;
+        cnt.close().map_err(OLMError::Io)?;
+        Ok(n)
+    }
+
+    pub fn build_from_map(
+        out_dir: &Path,
+        counts: &HashMap<CanonicalKmer, u32>,
+    ) -> OLMResult<usize> {
+        Self::build(out_dir, |kmer| counts.get(&kmer).copied().unwrap_or(0))
+    }
+}
+
 #[cfg(test)]
 #[path = "tests/layer.rs"]
 mod tests;

src/obilayeredmap/src/lib.rs

@@ -1,4 +1,3 @@
-pub mod counts;
 pub mod error;
 pub mod evidence;
 pub mod layer;
@@ -6,5 +5,5 @@ pub mod map;
 pub mod meta;
 
 pub use error::{OLMError, OLMResult};
-pub use layer::{Hit, Layer};
+pub use layer::{Hit, Layer, LayerData};
 pub use map::LayeredMap;

src/obilayeredmap/src/map.rs

@@ -2,11 +2,12 @@ use std::collections::HashMap;
 use std::fs;
 use std::path::{Path, PathBuf};
 
+use obicompactvec::PersistentCompactIntVec;
 use obikseq::CanonicalKmer;
 use obiskio::UnitigFileWriter;
 
 use crate::error::OLMResult;
-use crate::layer::{Hit, Layer};
+use crate::layer::{Hit, Layer, LayerData};
 use crate::meta::PartitionMeta;
 
 /// Layered kmer index for a single partition.
@@ -14,20 +15,26 @@ use crate::meta::PartitionMeta;
 /// Each layer covers a disjoint kmer set. Queries probe layers in order;
 /// the first match wins. Adding a dataset appends a new layer without
 /// rebuilding existing ones.
-pub struct LayeredMap {
-    root:   PathBuf,
-    meta:   PartitionMeta,
-    layers: Vec<Layer>,
+pub struct LayeredMap<D: LayerData = ()> {
+    root: PathBuf,
+    meta: PartitionMeta,
+    layers: Vec<Layer<D>>,
 }
 
-impl LayeredMap {
+// ── Common methods ────────────────────────────────────────────────────────────
+
+impl<D: LayerData> LayeredMap<D> {
     /// Open an existing layered index at `root`.
     pub fn open(root: &Path) -> OLMResult<Self> {
         let meta = PartitionMeta::load(root)?;
         let layers = (0..meta.n_layers)
-            .map(|i| Layer::open(&layer_dir(root, i)))
+            .map(|i| Layer::<D>::open(&layer_dir(root, i)))
             .collect::<OLMResult<Vec<_>>>()?;
-        Ok(Self { root: root.to_owned(), meta, layers })
+        Ok(Self {
+            root: root.to_owned(),
+            meta,
+            layers,
+        })
     }
 
     /// Create a new, empty layered index at `root`.
@@ -35,48 +42,71 @@ impl LayeredMap {
         fs::create_dir_all(root)?;
         let meta = PartitionMeta::new();
         meta.save(root)?;
-        Ok(Self { root: root.to_owned(), meta, layers: Vec::new() })
+        Ok(Self {
+            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 layer(&self, i: usize) -> &Layer {
+    /// 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)> {
-        self.layers.iter().enumerate().find_map(|(i, layer)| {
-            layer.query(kmer).map(|hit| (i, hit))
-        })
+    pub fn query(&self, kmer: CanonicalKmer) -> Option<(usize, Hit<D::Item>)> {
+        self.layers
+            .iter()
+            .enumerate()
+            .find_map(|(i, layer)| layer.query(kmer).map(|hit| (i, hit)))
     }
 
     /// Return a `UnitigFileWriter` for the next layer to be built.
-    /// The caller writes unitigs, calls `.close()` on the writer,
-    /// then calls `push_layer` to finish.
     pub fn next_layer_writer(&self) -> OLMResult<UnitigFileWriter> {
         let dir = layer_dir(&self.root, self.layers.len());
-        Layer::unitig_writer(&dir)
+        Layer::<D>::unitig_writer(&dir)
     }
 
-    /// Build and append the next layer from a count closure.
-    /// Unitigs must already have been written via `next_layer_writer`.
-    pub fn push_layer(
-        &mut self,
-        count_of: impl Fn(CanonicalKmer) -> u32,
-    ) -> OLMResult<usize> {
+    /// 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);
-        Layer::build(&dir, count_of)?;
-        self.layers.push(Layer::open(&dir)?);
+        self.layers.push(Layer::<D>::open(&dir)?);
         self.meta.n_layers = self.layers.len();
         self.meta.save(&self.root)?;
+        Ok(())
+    }
+}
+
+// ── Mode 1 — set membership ───────────────────────────────────────────────────
+
+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)?;
+        self.append_layer()?;
+        Ok(i)
+    }
+}
+
+// ── Mode 2 — counts ───────────────────────────────────────────────────────────
+
+impl LayeredMap<PersistentCompactIntVec> {
+    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::<PersistentCompactIntVec>::build(&dir, count_of)?;
+        self.append_layer()?;
         Ok(i)
     }
 
-    /// Convenience variant of `push_layer` that accepts a `HashMap`.
     pub fn push_layer_from_map(
         &mut self,
         counts: &HashMap<CanonicalKmer, u32>,

src/obilayeredmap/src/tests/layer.rs

@@ -1,4 +1,5 @@
 use super::*;
+use obicompactvec::PersistentCompactIntVec;
 use obikseq::{set_k, Kmer, Sequence as _, Unitig};
 use tempfile::tempdir;
 
@@ -28,8 +29,8 @@ fn build_and_query_all_kmers_found() {
     let dir = tempdir().unwrap();
     write_unitigs(dir.path(), &[b"AAAACGT"]);
     let kmers = all_canonical_kmers(dir.path(), 4);
-    Layer::build(dir.path(), |_| 1).unwrap();
-    let layer = Layer::open(dir.path()).unwrap();
+    Layer::<()>::build(dir.path()).unwrap();
+    let layer = Layer::<()>::open(dir.path()).unwrap();
     for kmer in kmers {
         assert!(layer.query(kmer).is_some(), "kmer should be present");
     }
@@ -43,11 +44,14 @@ fn counts_are_stored_and_retrieved() {
     let kmers = all_canonical_kmers(dir.path(), 4);
     let count_map: HashMap<CanonicalKmer, u32> =
         kmers.iter().enumerate().map(|(i, &k)| (k, i as u32 + 1)).collect();
-    Layer::build(dir.path(), |kmer| count_map.get(&kmer).copied().unwrap_or(0)).unwrap();
-    let layer = Layer::open(dir.path()).unwrap();
+    Layer::<PersistentCompactIntVec>::build(
+        dir.path(),
+        |kmer| count_map.get(&kmer).copied().unwrap_or(0),
+    ).unwrap();
+    let layer = Layer::<PersistentCompactIntVec>::open(dir.path()).unwrap();
     for kmer in &kmers {
         let hit = layer.query(*kmer).expect("kmer must be present");
-        assert_eq!(hit.count, count_map[kmer]);
+        assert_eq!(hit.data, count_map[kmer]);
     }
 }
 
@@ -56,8 +60,8 @@ fn query_absent_returns_none() {
     set_k(4);
     let dir = tempdir().unwrap();
     write_unitigs(dir.path(), &[b"AAAACGT"]);
-    Layer::build(dir.path(), |_| 1).unwrap();
-    let layer = Layer::open(dir.path()).unwrap();
+    Layer::<()>::build(dir.path()).unwrap();
+    let layer = Layer::<()>::open(dir.path()).unwrap();
     let absent = Kmer::from_ascii(b"CCCC").unwrap().canonical();
     assert!(layer.query(absent).is_none());
 }
@@ -66,12 +70,11 @@ fn query_absent_returns_none() {
 fn open_after_build_is_consistent() {
     set_k(4);
     let dir = tempdir().unwrap();
-    // "AAAACGT": 7 nucl → 4 kmers, all with distinct canonical forms
     write_unitigs(dir.path(), &[b"AAAACGT"]);
-    let n = Layer::build(dir.path(), |_| 7).unwrap();
+    let n = Layer::<PersistentCompactIntVec>::build(dir.path(), |_| 7).unwrap();
     assert_eq!(n, 4);
-    let layer = Layer::open(dir.path()).unwrap();
+    let layer = Layer::<PersistentCompactIntVec>::open(dir.path()).unwrap();
     let kmer = Kmer::from_ascii(b"AAAA").unwrap().canonical();
     let hit = layer.query(kmer).expect("AAAA must be present");
-    assert_eq!(hit.count, 7);
+    assert_eq!(hit.data, 7);
 }

src/obilayeredmap/src/tests/map.rs

@@ -1,9 +1,10 @@
 use super::*;
+use obicompactvec::PersistentCompactIntVec;
 use obikseq::{set_k, Sequence as _, Unitig};
 use tempfile::tempdir;
 
 fn push_unitigs_and_layer(
-    map: &mut LayeredMap,
+    map: &mut LayeredMap<PersistentCompactIntVec>,
     seqs: &[&[u8]],
     count: u32,
 ) {
@@ -23,7 +24,7 @@ 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()).unwrap();
     assert_eq!(map.n_layers(), 0);
 }
 
@@ -32,10 +33,10 @@ fn open_reloads_layer_count() {
     set_k(4);
     let dir = tempdir().unwrap();
     {
-        let mut map = LayeredMap::create(dir.path()).unwrap();
+        let mut map = LayeredMap::<PersistentCompactIntVec>::create(dir.path()).unwrap();
         push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
     }
-    let map = LayeredMap::open(dir.path()).unwrap();
+    let map = LayeredMap::<PersistentCompactIntVec>::open(dir.path()).unwrap();
     assert_eq!(map.n_layers(), 1);
 }
 
@@ -43,41 +44,37 @@ fn open_reloads_layer_count() {
 fn query_finds_kmer_in_layer_zero() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::create(dir.path()).unwrap();
+    let mut map = LayeredMap::<PersistentCompactIntVec>::create(dir.path()).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");
     assert_eq!(layer_idx, 0);
-    assert_eq!(hit.count, 3);
+    assert_eq!(hit.data, 3);
 }
 
 #[test]
 fn query_finds_kmer_in_correct_layer() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::create(dir.path()).unwrap();
-    // Layer 0: AAAACGT
+    let mut map = LayeredMap::<PersistentCompactIntVec>::create(dir.path()).unwrap();
     push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
-    // Layer 1: GGGACGT  (no kmer overlap with layer 0 by construction)
     push_unitigs_and_layer(&mut map, &[b"GGGACGT"], 2);
     assert_eq!(map.n_layers(), 2);
 
-    // AAAA is in layer 0
     let (li, hit) = map.query(canonical(b"AAAA")).expect("AAAA must be found");
     assert_eq!(li, 0);
-    assert_eq!(hit.count, 1);
+    assert_eq!(hit.data, 1);
 
-    // GGGA is in layer 1
     let (li, hit) = map.query(canonical(b"GGGA")).expect("GGGA must be found");
     assert_eq!(li, 1);
-    assert_eq!(hit.count, 2);
+    assert_eq!(hit.data, 2);
 }
 
 #[test]
 fn query_absent_returns_none() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::create(dir.path()).unwrap();
+    let mut map = LayeredMap::<PersistentCompactIntVec>::create(dir.path()).unwrap();
     push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
     let absent = canonical(b"CCCC");
     assert!(map.query(absent).is_none());
@@ -87,7 +84,7 @@ fn query_absent_returns_none() {
 fn push_layer_from_map_convenience() {
     set_k(4);
     let dir = tempdir().unwrap();
-    let mut map = LayeredMap::create(dir.path()).unwrap();
+    let mut map = LayeredMap::<PersistentCompactIntVec>::create(dir.path()).unwrap();
     let mut w = map.next_layer_writer().unwrap();
     w.write(&Unitig::from_ascii(b"AAAACGT")).unwrap();
     w.close().unwrap();
@@ -96,5 +93,5 @@ fn push_layer_from_map_convenience() {
     ].into_iter().collect();
     map.push_layer_from_map(&counts).unwrap();
     let (_, hit) = map.query(canonical(b"AAAA")).unwrap();
-    assert_eq!(hit.count, 10);
+    assert_eq!(hit.data, 10);
 }