Introduce compare_sparse CLI tool to verify index consistency

Adds a new binary that validates bit-level consistency between dense and sparse K-mer index representations by sampling slots across partitions and reporting discrepancies. Refactors sibling cache matrix initialization into a centralized factory method to simplify control flow and standardize error handling. Introduces diagnostic configurations, benchmark scripts, and an ignored test case to support k-mer resolution analysis.

src/obikphylo/src/siblings/family_scan.rs

@@ -53,9 +53,7 @@ use std::sync::atomic::{AtomicU8, Ordering};
 
 use rayon::prelude::*;
 
-use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
 use obikseq::CanonicalKmer;
-use obilayeredmap::Layer;
 use obilayeredmap::meta::PartitionMeta;
 use obipipeline::{ThrottleGuard, throttle};
 
@@ -195,12 +193,7 @@ pub(super) fn scan_layer_families(
     let meta = PartitionMeta::load(index_dir).map_err(olm_to_ok)?;
     let annex = Arc::new(SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?);
 
-    let use_counts = with_counts && layer_dir.join("counts").exists();
-    let mat = if use_counts {
-        Mat::Count(Layer::<PersistentCompactIntMatrix>::open(layer_dir, &meta.mode).map_err(olm_to_ok)?)
-    } else {
-        Mat::Presence(Layer::<PersistentBitMatrix>::open(layer_dir, &meta.mode).map_err(olm_to_ok)?)
-    };
+    let mat = Mat::open(layer_dir, &meta.mode, with_counts).map_err(olm_to_ok)?;
     let n_cols = mat.n_cols().min(n_genomes);
 
     let ctx = Arc::new(LayerCtx { mat, n_parts, n_genomes, n_cols, k });