feat: centralize index configuration and add hybrid mode

Centralizes index configuration by storing a single `IndexMode` (`Exact`, `Approx`, or `Hybrid`) in `PartitionMeta`, eliminating per-layer metadata files. Introduces a `Hybrid` evidence mode and an `--approx` CLI flag to toggle between exact and probabilistic indexing. Refactors the build and query pipelines to dynamically dispatch based on the configured mode, deferring `.idx` generation to Pass 2 and only requiring it for Exact/Hybrid modes. Updates layer opening to load appropriate data structures, enforces strict parameter validation during merges, and clarifies performance trade-offs in documentation.

src/obikindex/src/merge.rs

@@ -9,7 +9,7 @@ use obisys::{Reporter, Stage};
 use rayon::prelude::*;
 use tracing::info;
 
-use obilayeredmap::EvidenceKind;
+use obilayeredmap::IndexMode;
 
 use crate::error::{OKIError, OKIResult};
 use crate::index::KmerIndex;
@@ -271,14 +271,16 @@ fn partition_bar(n: u64) -> ProgressBar {
 /// - all `Exact`                        → OK, returns `Exact`
 /// - all `Approx { b, z }` same params  → OK, returns `Approx { b, z }`
 /// - mixed exact/approx or different approx params → `IncompatibleEvidence`
-fn validate_evidence_compat(sources: &[&KmerIndex]) -> OKIResult<EvidenceKind> {
+fn validate_evidence_compat(sources: &[&KmerIndex]) -> OKIResult<IndexMode> {
     let ref_ev = &sources[0].meta.config.evidence;
     for src in &sources[1..] {
         let ev = &src.meta.config.evidence;
         let compat = match (ref_ev, ev) {
-            (EvidenceKind::Exact, EvidenceKind::Exact) => true,
-            (EvidenceKind::Approx { b: b1, z: z1 },
-             EvidenceKind::Approx { b: b2, z: z2 }) => b1 == b2 && z1 == z2,
+            (IndexMode::Exact, IndexMode::Exact) => true,
+            (IndexMode::Approx { b: b1, z: z1 },
+             IndexMode::Approx { b: b2, z: z2 }) => b1 == b2 && z1 == z2,
+            (IndexMode::Hybrid { b: b1, z: z1 },
+             IndexMode::Hybrid { b: b2, z: z2 }) => b1 == b2 && z1 == z2,
             _ => false,
         };
         if !compat {

src/obikindex/src/meta.rs

@@ -3,7 +3,7 @@ use std::fs;
 use std::io;
 use std::path::Path;
 
-use obilayeredmap::EvidenceKind;
+use obilayeredmap::IndexMode;
 use serde::{Deserialize, Serialize};
 
 pub const META_FILENAME: &str = "index.meta";
@@ -30,7 +30,7 @@ pub struct IndexConfig {
     pub n_bits: usize,
     pub with_counts: bool,
     #[serde(default)]
-    pub evidence: EvidenceKind,
+    pub evidence: IndexMode,
     /// Block size for the unitig index as a power-of-two exponent.
     /// The `.idx` block covers 2^block_bits consecutive unitigs.
     /// 0 = one entry per unitig (O(1) access, largest `.idx`).

src/obikindex/src/reindex.rs

@@ -3,7 +3,7 @@ use std::path::Path;
 use std::time::Duration;
 
 use indicatif::{ProgressBar, ProgressStyle};
-use obilayeredmap::{EvidenceKind, layer::Layer};
+use obilayeredmap::{IndexMode, layer::Layer};
 use obilayeredmap::meta::PartitionMeta;
 use obisys::{Reporter, Stage};
 use rayon::prelude::*;
@@ -31,7 +31,7 @@ impl KmerIndex {
     /// `index.meta` is updated with the new evidence kind on success.
     pub fn reindex(
         &mut self,
-        target: EvidenceKind,
+        target: IndexMode,
         block_bits: u8,
         rep: &mut Reporter,
     ) -> OKIResult<()> {
@@ -75,7 +75,7 @@ impl KmerIndex {
         }
 
         self.meta.config.evidence = target;
-        if matches!(self.meta.config.evidence, EvidenceKind::Exact) {
+        if matches!(self.meta.config.evidence, IndexMode::Exact) {
             self.meta.config.block_bits = block_bits;
         }
         self.meta.write(&self.root_path)?;
@@ -85,7 +85,7 @@ impl KmerIndex {
 }
 
 /// Process all layers of one partition's index directory.
-fn reindex_partition(index_dir: &Path, target: &EvidenceKind, block_bits: u8) -> OKIResult<()> {
+fn reindex_partition(index_dir: &Path, target: &IndexMode, block_bits: u8) -> OKIResult<()> {
     if !index_dir.exists() {
         return Ok(());
     }
@@ -97,22 +97,30 @@ fn reindex_partition(index_dir: &Path, target: &EvidenceKind, block_bits: u8) ->
     Ok(())
 }
 
-fn reindex_layer(layer_dir: &Path, target: &EvidenceKind, block_bits: u8) -> OKIResult<()> {
-    Layer::<()>::build_evidence(layer_dir, target, block_bits).map_err(olm_to_oki)?;
+fn reindex_layer(layer_dir: &Path, target: &IndexMode, block_bits: u8) -> OKIResult<()> {
+    match target {
+        IndexMode::Exact => {
+            Layer::<()>::build_exact_evidence(layer_dir, block_bits).map_err(olm_to_oki)?;
+        }
+        IndexMode::Approx { b, z } | IndexMode::Hybrid { b, z } => {
+            Layer::<()>::build_approx_evidence(layer_dir, *b, *z).map_err(olm_to_oki)?;
+        }
+    }
     remove_stale_evidence(layer_dir, target)
 }
 
-fn remove_stale_evidence(layer_dir: &Path, target: &EvidenceKind) -> OKIResult<()> {
+fn remove_stale_evidence(layer_dir: &Path, target: &IndexMode) -> OKIResult<()> {
     match target {
-        EvidenceKind::Exact => {
-            // fingerprint.bin is no longer valid
+        IndexMode::Exact => {
             remove_if_exists(&layer_dir.join(FINGERPRINT_FILE));
         }
-        EvidenceKind::Approx { .. } => {
-            // exact bundle is no longer valid
+        IndexMode::Approx { .. } => {
             remove_if_exists(&layer_dir.join(EVIDENCE_FILE));
             remove_if_exists(&layer_dir.join(UNITIG_IDX_FILE));
         }
+        IndexMode::Hybrid { .. } => {
+            // both bundles kept — nothing to remove
+        }
     }
     Ok(())
 }