feat: add obilayeredmap crate for disk-backed k-mer indexing

Introduces the `obilayeredmap` crate (v0.1.0), implementing an append-only, disk-backed k-mer index using a minimal perfect hash function (MPHF). The module features memory-mapped reads, buffered writes, custom error handling, partition metadata persistence, and comprehensive unit tests. Also adds a reverse complement benchmark for `obikseq` and updates `Cargo.lock` with the new dependencies.

src/Cargo.lock

@@ -1649,6 +1649,19 @@ dependencies = [
  "xxhash-rust",
 ]
 
+[[package]]
+name = "obilayeredmap"
+version = "0.1.0"
+dependencies = [
+ "memmap2",
+ "obikseq",
+ "obiskio",
+ "ph",
+ "serde",
+ "serde_json",
+ "tempfile",
+]
+
 [[package]]
 name = "obipipeline"
 version = "0.1.0"

src/Cargo.toml

@@ -1,5 +1,5 @@
 [workspace]
 resolver = "3"
-members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj"]
+members = ["obikseq", "obiread", "obiskbuilder", "obifastwrite", "obikmer","obikrope","obipipeline", "obikpartitionner","obiskio","obidebruinj","obilayeredmap"]
 [profile.release]
 debug = 1

src/obikseq/benches/superkmer.rs

@@ -1,5 +1,7 @@
 use criterion::{BatchSize, BenchmarkId, Criterion, Throughput, criterion_group, criterion_main};
+use obikseq::packed_seq::PackedSeq;
 use obikseq::superkmer::SuperKmer;
+use obikseq::Sequence;
 
 const LENGTHS: &[usize] = &[1, 4, 8, 16, 40, 64, 128, 255, 256];
 
@@ -50,12 +52,12 @@ fn bench_write_ascii(c: &mut Criterion) {
 fn bench_revcomp(c: &mut Criterion) {
     let mut group = c.benchmark_group("revcomp");
     for &len in LENGTHS {
-        let sk = SuperKmer::from_ascii(&make_ascii(len));
+        let seq = PackedSeq::from_ascii(&make_ascii(len));
         group.throughput(Throughput::Bytes(len as u64));
-        group.bench_with_input(BenchmarkId::from_parameter(len), &sk, |b, sk| {
+        group.bench_with_input(BenchmarkId::from_parameter(len), &seq, |b, seq| {
             b.iter_batched(
-                || sk.clone(),
-                |mut s| { std::hint::black_box(&mut s).revcomp(); s },
+                || seq.clone(),
+                |s| { let mut s = std::hint::black_box(s); s.revcomp_inplace(); s },
                 BatchSize::SmallInput,
             );
         });

src/obilayeredmap/Cargo.toml

@@ -0,0 +1,16 @@
+[package]
+name = "obilayeredmap"
+version = "0.1.0"
+edition = "2024"
+
+[dependencies]
+obikseq  = { path = "../obikseq" }
+obiskio  = { path = "../obiskio" }
+ph = "0.11"
+memmap2  = "0.9"
+serde      = { version = "1", features = ["derive"] }
+serde_json = "1"
+
+[dev-dependencies]
+tempfile = "3"
+obikseq = { path = "../obikseq", features = ["test-utils"] }

src/obilayeredmap/src/counts.rs

@@ -0,0 +1,54 @@
+// 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/error.rs

@@ -0,0 +1,50 @@
+use std::fmt;
+use std::io;
+
+#[derive(Debug)]
+pub enum OLMError {
+    Io(io::Error),
+    Json(serde_json::Error),
+    Mphf(String),
+    InvalidLayer(String),
+}
+
+pub type OLMResult<T> = Result<T, OLMError>;
+
+impl fmt::Display for OLMError {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        match self {
+            OLMError::Io(e)            => write!(f, "I/O error: {e}"),
+            OLMError::Json(e)          => write!(f, "JSON error: {e}"),
+            OLMError::Mphf(s)          => write!(f, "MPHF error: {s}"),
+            OLMError::InvalidLayer(s)  => write!(f, "invalid layer: {s}"),
+        }
+    }
+}
+
+impl std::error::Error for OLMError {
+    fn source(&self) -> Option<&(dyn std::error::Error + 'static)> {
+        match self {
+            OLMError::Io(e)   => Some(e),
+            OLMError::Json(e) => Some(e),
+            _                 => None,
+        }
+    }
+}
+
+impl From<io::Error> for OLMError {
+    fn from(e: io::Error) -> Self { OLMError::Io(e) }
+}
+
+impl From<serde_json::Error> for OLMError {
+    fn from(e: serde_json::Error) -> Self { OLMError::Json(e) }
+}
+
+impl From<obiskio::SKError> for OLMError {
+    fn from(e: obiskio::SKError) -> Self {
+        match e {
+            obiskio::SKError::Io(io_err) => OLMError::Io(io_err),
+            other => OLMError::InvalidLayer(other.to_string()),
+        }
+    }
+}

src/obilayeredmap/src/evidence.rs

@@ -0,0 +1,60 @@
+// u32 per MPHF slot: bits [31:7] = chunk_id (25 bits), bits [6:0] = rank (7 bits).
+
+use std::fs::File;
+use std::io::{BufWriter, Write};
+use std::path::Path;
+
+use memmap2::Mmap;
+
+use crate::error::{OLMError, OLMResult};
+
+pub struct Evidence {
+    mmap: Mmap,
+}
+
+impl Evidence {
+    pub fn open(path: &Path) -> OLMResult<Self> {
+        let f = File::open(path)?;
+        let mmap = unsafe { Mmap::map(&f)? };
+        Ok(Self { mmap })
+    }
+
+    #[inline]
+    pub fn decode(&self, slot: usize) -> (u32, u8) {
+        let off = slot * 4;
+        let raw = u32::from_le_bytes(self.mmap[off..off + 4].try_into().unwrap());
+        (raw >> 7, (raw & 0x7F) as u8)
+    }
+
+    pub fn len(&self) -> usize {
+        self.mmap.len() / 4
+    }
+}
+
+#[inline]
+pub fn encode(chunk_id: u32, rank: u8) -> u32 {
+    (chunk_id << 7) | (rank as u32 & 0x7F)
+}
+
+pub struct EvidenceWriter {
+    buf: Vec<u32>,
+}
+
+impl EvidenceWriter {
+    pub fn new(n_slots: usize) -> Self {
+        Self { buf: vec![0u32; n_slots] }
+    }
+
+    #[inline]
+    pub fn set(&mut self, slot: usize, chunk_id: u32, rank: u8) {
+        self.buf[slot] = encode(chunk_id, rank);
+    }
+
+    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

@@ -0,0 +1,122 @@
+use std::collections::HashMap;
+use std::fs;
+use std::io::BufWriter;
+use std::path::Path;
+
+use obikseq::{CanonicalKmer, Kmer, Sequence};
+use obiskio::{UnitigFileReader, UnitigFileWriter};
+use ph::fmph;
+
+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";
+const EVIDENCE_FILE: &str = "evidence.bin";
+const COUNTS_FILE:   &str = "counts.bin";
+
+pub struct Layer {
+    mphf:     fmph::Function,
+    evidence: Evidence,
+    unitigs:  UnitigFileReader,
+    counts:   Counts,
+}
+
+pub struct Hit {
+    pub slot:  usize,
+    pub count: u32,
+}
+
+impl Layer {
+    pub fn open(path: &Path) -> OLMResult<Self> {
+        let mphf = fmph::Function::read(
+            &mut fs::File::open(path.join(MPHF_FILE))?
+        ).map_err(OLMError::Io)?;
+
+        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 })
+    }
+
+    pub fn query(&self, kmer: CanonicalKmer) -> Option<Hit> {
+        let slot = self.mphf.get(&kmer.raw())? as usize;
+        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) })
+        } 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> {
+        let k = obikseq::params::k();
+        let unitigs = UnitigFileReader::open(&out_dir.join(UNITIGS_FILE))?;
+
+        let mut entries: Vec<(u64, u32, u8)> = Vec::new();
+        for chunk_id in 0..unitigs.len() {
+            let n_kmers = unitigs.seql(chunk_id) - k + 1;
+            for rank in 0..n_kmers {
+                let raw = unitigs.raw_kmer(chunk_id, rank);
+                let canonical: CanonicalKmer = Kmer::from_raw(raw).canonical();
+                entries.push((canonical.raw(), chunk_id as u32, rank as u8));
+            }
+        }
+
+        let n = entries.len();
+        if n == 0 {
+            fs::File::create(out_dir.join(EVIDENCE_FILE))?;
+            fs::File::create(out_dir.join(COUNTS_FILE))?;
+            let mphf = fmph::Function::new(Vec::<u64>::new());
+            mphf.write(&mut BufWriter::new(fs::File::create(out_dir.join(MPHF_FILE))?))?;
+            return Ok(0);
+        }
+
+        let keys: Vec<u64> = entries.iter().map(|(k, _, _)| *k).collect();
+        let mphf = fmph::Function::new(keys);
+        mphf.write(&mut BufWriter::new(fs::File::create(out_dir.join(MPHF_FILE))?))?;
+
+        let mut ev  = EvidenceWriter::new(n);
+        let mut cnt = CountsWriter::new(n);
+
+        for (key, chunk_id, rank) in &entries {
+            let slot = mphf.get(key).unwrap() as usize;
+            ev.set(slot, *chunk_id, *rank);
+            let kmer = CanonicalKmer::from_raw_unchecked(*key);
+            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))?)
+    }
+}
+
+#[cfg(test)]
+#[path = "tests/layer.rs"]
+mod tests;

src/obilayeredmap/src/lib.rs

@@ -0,0 +1,10 @@
+pub mod counts;
+pub mod error;
+pub mod evidence;
+pub mod layer;
+pub mod map;
+pub mod meta;
+
+pub use error::{OLMError, OLMResult};
+pub use layer::{Hit, Layer};
+pub use map::LayeredMap;

src/obilayeredmap/src/map.rs

@@ -0,0 +1,94 @@
+use std::collections::HashMap;
+use std::fs;
+use std::path::{Path, PathBuf};
+
+use obikseq::CanonicalKmer;
+use obiskio::UnitigFileWriter;
+
+use crate::error::OLMResult;
+use crate::layer::{Hit, Layer};
+use crate::meta::PartitionMeta;
+
+/// Layered kmer index for a single partition.
+///
+/// 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>,
+}
+
+impl LayeredMap {
+    /// 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)))
+            .collect::<OLMResult<Vec<_>>>()?;
+        Ok(Self { root: root.to_owned(), meta, layers })
+    }
+
+    /// Create a new, empty layered index at `root`.
+    pub fn create(root: &Path) -> OLMResult<Self> {
+        fs::create_dir_all(root)?;
+        let meta = PartitionMeta::new();
+        meta.save(root)?;
+        Ok(Self { root: root.to_owned(), meta, layers: Vec::new() })
+    }
+
+    pub fn n_layers(&self) -> usize {
+        self.layers.len()
+    }
+
+    pub fn layer(&self, i: usize) -> &Layer {
+        &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))
+        })
+    }
+
+    /// 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)
+    }
+
+    /// 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> {
+        let i = self.layers.len();
+        let dir = layer_dir(&self.root, i);
+        Layer::build(&dir, count_of)?;
+        self.layers.push(Layer::open(&dir)?);
+        self.meta.n_layers = self.layers.len();
+        self.meta.save(&self.root)?;
+        Ok(i)
+    }
+
+    /// Convenience variant of `push_layer` that accepts a `HashMap`.
+    pub fn push_layer_from_map(
+        &mut self,
+        counts: &HashMap<CanonicalKmer, u32>,
+    ) -> OLMResult<usize> {
+        self.push_layer(|kmer| counts.get(&kmer).copied().unwrap_or(0))
+    }
+}
+
+fn layer_dir(root: &Path, i: usize) -> PathBuf {
+    root.join(format!("layer_{i}"))
+}
+
+#[cfg(test)]
+#[path = "tests/map.rs"]
+mod tests;

src/obilayeredmap/src/meta.rs

@@ -0,0 +1,34 @@
+use std::fs::File;
+use std::path::Path;
+
+use serde::{Deserialize, Serialize};
+
+use crate::error::OLMResult;
+
+const META_FILE: &str = "meta.json";
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct PartitionMeta {
+    pub n_layers: usize,
+}
+
+impl PartitionMeta {
+    pub fn new() -> Self {
+        Self { n_layers: 0 }
+    }
+
+    pub fn load(dir: &Path) -> OLMResult<Self> {
+        let f = File::open(dir.join(META_FILE))?;
+        Ok(serde_json::from_reader(f)?)
+    }
+
+    pub fn save(&self, dir: &Path) -> OLMResult<()> {
+        let f = File::create(dir.join(META_FILE))?;
+        serde_json::to_writer_pretty(f, self)?;
+        Ok(())
+    }
+}
+
+impl Default for PartitionMeta {
+    fn default() -> Self { Self::new() }
+}

src/obilayeredmap/src/tests/layer.rs

@@ -0,0 +1,77 @@
+use super::*;
+use obikseq::{set_k, Unitig};
+use tempfile::tempdir;
+
+fn write_unitigs(dir: &Path, seqs: &[&[u8]]) {
+    let mut w = UnitigFileWriter::create(&dir.join(UNITIGS_FILE)).unwrap();
+    for s in seqs {
+        w.write(&Unitig::from_ascii(s)).unwrap();
+    }
+    w.close().unwrap();
+}
+
+fn all_canonical_kmers(dir: &Path, k: usize) -> Vec<CanonicalKmer> {
+    let r = UnitigFileReader::open(&dir.join(UNITIGS_FILE)).unwrap();
+    let mut out = Vec::new();
+    for ci in 0..r.len() {
+        let n = r.seql(ci) - k + 1;
+        for rank in 0..n {
+            out.push(Kmer::from_raw(r.raw_kmer(ci, rank)).canonical());
+        }
+    }
+    out
+}
+
+#[test]
+fn build_and_query_all_kmers_found() {
+    set_k(4);
+    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();
+    for kmer in kmers {
+        assert!(layer.query(kmer).is_some(), "kmer should be present");
+    }
+}
+
+#[test]
+fn counts_are_stored_and_retrieved() {
+    set_k(4);
+    let dir = tempdir().unwrap();
+    write_unitigs(dir.path(), &[b"AAAACGT"]);
+    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();
+    for kmer in &kmers {
+        let hit = layer.query(*kmer).expect("kmer must be present");
+        assert_eq!(hit.count, count_map[kmer]);
+    }
+}
+
+#[test]
+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();
+    let absent = Kmer::from_ascii(b"CCCC").unwrap().canonical();
+    assert!(layer.query(absent).is_none());
+}
+
+#[test]
+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();
+    assert_eq!(n, 4);
+    let layer = Layer::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);
+}

src/obilayeredmap/src/tests/map.rs

@@ -0,0 +1,100 @@
+use super::*;
+use obikseq::{set_k, Sequence as _, Unitig};
+use tempfile::tempdir;
+
+fn push_unitigs_and_layer(
+    map: &mut LayeredMap,
+    seqs: &[&[u8]],
+    count: u32,
+) {
+    let mut w = map.next_layer_writer().unwrap();
+    for s in seqs {
+        w.write(&Unitig::from_ascii(s)).unwrap();
+    }
+    w.close().unwrap();
+    map.push_layer(|_| count).unwrap();
+}
+
+fn canonical(ascii: &[u8]) -> CanonicalKmer {
+    obikseq::Kmer::from_ascii(ascii).unwrap().canonical()
+}
+
+#[test]
+fn create_empty_map() {
+    set_k(4);
+    let dir = tempdir().unwrap();
+    let map = LayeredMap::create(dir.path()).unwrap();
+    assert_eq!(map.n_layers(), 0);
+}
+
+#[test]
+fn open_reloads_layer_count() {
+    set_k(4);
+    let dir = tempdir().unwrap();
+    {
+        let mut map = LayeredMap::create(dir.path()).unwrap();
+        push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
+    }
+    let map = LayeredMap::open(dir.path()).unwrap();
+    assert_eq!(map.n_layers(), 1);
+}
+
+#[test]
+fn query_finds_kmer_in_layer_zero() {
+    set_k(4);
+    let dir = tempdir().unwrap();
+    let mut map = LayeredMap::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);
+}
+
+#[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
+    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);
+
+    // 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);
+}
+
+#[test]
+fn query_absent_returns_none() {
+    set_k(4);
+    let dir = tempdir().unwrap();
+    let mut map = LayeredMap::create(dir.path()).unwrap();
+    push_unitigs_and_layer(&mut map, &[b"AAAACGT"], 1);
+    let absent = canonical(b"CCCC");
+    assert!(map.query(absent).is_none());
+}
+
+#[test]
+fn push_layer_from_map_convenience() {
+    set_k(4);
+    let dir = tempdir().unwrap();
+    let mut map = LayeredMap::create(dir.path()).unwrap();
+    let mut w = map.next_layer_writer().unwrap();
+    w.write(&Unitig::from_ascii(b"AAAACGT")).unwrap();
+    w.close().unwrap();
+    let counts: HashMap<CanonicalKmer, u32> = vec![
+        (canonical(b"AAAA"), 10u32),
+    ].into_iter().collect();
+    map.push_layer_from_map(&counts).unwrap();
+    let (_, hit) = map.query(canonical(b"AAAA")).unwrap();
+    assert_eq!(hit.count, 10);
+}