TODO.md

@@ -1,3 +1,21 @@
+## A finir dans le cadre de l'extension des index à une forme approximative
+
+- Il faut avoir un chemin explicite pour construire en mode exact avec des méthodes qui ont ce mot exact à l'intérieur.
+  - pub fn find_exact (src/obilayeredmap/src/mphf_layer.rs)
+  - pub fn build_exact_evidence (src/obilayeredmap/src/layer.rs)
+
+Comme elles existent actuellement pour le mode approx.
+
+Ensuite, il faudra définir des méthodes génériques
+- find()
+- build_evidence()
+
+qui utilise la bonne version suivant le mode de l'index de manière complètement transparente.
+Avec ce système, tout le reste du code devrait être insensible au fait que l'on utilise un index exact ou approximatif.
+
+Sauf qu'avec un index approximatif, les résultats seront approximatifs.
+
+
 ## commandes à ajouter
 
 - aggregate : aggrege toutes les colonnes d'une matrice d'index en une seule colonne.

src/obikindex/src/meta.rs

@@ -3,6 +3,7 @@ use std::fs;
 use std::io;
 use std::path::Path;
 
+use obilayeredmap::EvidenceKind;
 use serde::{Deserialize, Serialize};
 
 pub const META_FILENAME: &str = "index.meta";
@@ -28,6 +29,8 @@ pub struct IndexConfig {
     pub minimizer_size: usize,
     pub n_bits: usize,
     pub with_counts: bool,
+    #[serde(default)]
+    pub evidence: EvidenceKind,
 }
 
 #[derive(Debug, Clone, Serialize, Deserialize)]

src/obilayeredmap/src/layer.rs

@@ -86,11 +86,12 @@ impl<D: LayerData> Layer<D> {
     }
 
     /// Build `fingerprint.bin` from `unitigs.bin` and `mphf.bin` already
-    /// present in `layer_dir`.  `b` is the fingerprint width in bits (1..=64).
+    /// present in `layer_dir`.  `b` — fingerprint bits (1..=64); `z` — Findere
+    /// consecutive k-mer parameter (≥1).
     ///
     /// See [`MphfLayer::build_approx_evidence`] for the full contract.
-    pub fn build_approx_evidence(layer_dir: &Path, b: u8) -> OLMResult<usize> {
+    pub fn build_approx_evidence(layer_dir: &Path, b: u8, z: u8) -> OLMResult<usize> {
-        MphfLayer::build_approx_evidence(layer_dir, b)
+        MphfLayer::build_approx_evidence(layer_dir, b, z)
     }
 }
 

src/obilayeredmap/src/lib.rs

@@ -11,4 +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 mphf_layer::MphfLayer;

src/obilayeredmap/src/meta.rs

@@ -5,7 +5,55 @@ 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 ──────────────────────────────────────────────────────
+
+/// Describes the evidence bundle stored alongside the MPHF for one layer.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+#[serde(tag = "type", rename_all = "snake_case")]
+pub enum EvidenceKind {
+    /// 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 = 1/2^b.
+    /// `z` — consecutive k-mers that must all match (Findere trick);
+    ///        effective FP rate per read ≈ (W / 2^(b*z)) where W = read windows.
+    Approx { b: u8, z: u8 },
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct LayerMeta {
+    pub evidence: EvidenceKind,
+}
+
+impl Default for EvidenceKind {
+    fn default() -> Self { Self::Exact }
+}
+
+impl LayerMeta {
+    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 ──────────────────────────────────────────────────
 
 #[derive(Debug, Clone, Serialize, Deserialize)]
 pub struct PartitionMeta {

src/obilayeredmap/src/mphf_layer.rs

@@ -10,6 +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::LayerMeta;
 
 pub(crate) const MPHF_FILE:        &str = "mphf.bin";
 pub(crate) const UNITIGS_FILE:     &str = "unitigs.bin";
@@ -118,24 +119,30 @@ impl MphfLayer {
         ev.write(&dir.join(EVIDENCE_FILE))?;
         // Write .idx last: it is only needed for random access (queries).
         build_unitig_idx(&unitig_path, DEFAULT_BLOCK_BITS)?;
+        LayerMeta::exact().save(dir)?;
         Ok(n)
     }
 
     /// Build `fingerprint.bin` from `unitigs.bin` and `mphf.bin` already present
-    /// in `dir`.  `b` is the number of fingerprint bits (1..=64).
+    /// in `dir`.  `b` — fingerprint bits (1..=64); `z` — Findere consecutive
+    /// k-mer parameter (≥1).
     ///
     /// The fingerprint for each slot is the low `b` bits of `kmer.seq_hash()`.
     /// No `.idx` file is written — approximate evidence needs no random access.
-    pub fn build_approx_evidence(dir: &Path, b: u8) -> OLMResult<usize> {
+    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()));
         }
+        if z == 0 {
+            return Err(OLMError::InvalidLayer("z must be ≥ 1".into()));
+        }
         let unitig_path = dir.join(UNITIGS_FILE);
         let unitigs = UnitigFileReader::open_sequential(&unitig_path)?;
         let n = unitigs.n_kmers();
 
         if n == 0 {
             FingerprintVecWriter::new(0, b).write(&dir.join(FINGERPRINT_FILE))?;
+            LayerMeta::approx(b, z).save(dir)?;
             return Ok(0);
         }
 
@@ -153,6 +160,7 @@ impl MphfLayer {
         }
 
         fw.write(&dir.join(FINGERPRINT_FILE))?;
+        LayerMeta::approx(b, z).save(dir)?;
         Ok(n)
     }
 
@@ -214,6 +222,7 @@ impl MphfLayer {
         }
 
         ev.write(&dir.join(EVIDENCE_FILE))?;
+        LayerMeta::exact().save(dir)?;
         Ok(n)
     }
 }