Add unitig streaming iterators and estimate CLI subcommand

Introduce `iter_unitigs` methods across the index cache, content layer, MphfLayer, and typed layer to stream whole reconstructed sequences directly from underlying storage without decomposing into k-mers. Add a corresponding low-level streaming iterator in obiskio for thread-safe, lazy reads from memory-mapped files. Include a new CLI subcommand to compute and display approximate false-positive rates based on provided indexing parameters.

src/obikmer2/src/cmd/estimate/mod.rs

@@ -0,0 +1,38 @@
+use clap::Args;
+
+use super::index::resolve_approx_params;
+
+#[derive(Args)]
+pub struct EstimateArgs {
+    /// k-mer size used for querying (same as --kmer-size in index)
+    #[arg(short = 'k', long, default_value_t = 31)]
+    pub kmer_size: usize,
+
+    /// Findere z parameter: number of consecutive k-mers that must all match.
+    /// Effective indexed k-mer size is kmer_size - z + 1.
+    #[arg(short = 'z', long, default_value = None)]
+    pub findere_z: Option<u8>,
+
+    /// Fingerprint bits per slot (b).  FP per z-window = 1/2^(b·z).
+    #[arg(long, default_value = None)]
+    pub evidence_bits: Option<u8>,
+
+    /// Target false-positive rate per z-window (e.g. 0.01).
+    #[arg(long, default_value = None)]
+    pub fp: Option<f64>,
+}
+
+pub fn run(args: EstimateArgs) {
+    let (z, b, fp_window) = resolve_approx_params(args.findere_z, args.evidence_bits, args.fp);
+
+    let k_query = args.kmer_size;
+    let k_index = k_query.saturating_sub(z as usize - 1);
+    let fp_kmer = 1.0_f64 / 2_f64.powi(b as i32);
+
+    println!("{:<22} {}", "k (query):",        k_query);
+    println!("{:<22} {}", "k (indexed):",      k_index);
+    println!("{:<22} {}", "z:",                z);
+    println!("{:<22} {}", "evidence bits (b):", b);
+    println!("{:<22} {:.3e}  (1/2^{})",        "FP per k-mer:",    fp_kmer,   b);
+    println!("{:<22} {:.3e}  (1/2^{})",        "FP per z-window:", fp_window, b as u32 * z as u32);
+}

src/obikmer2/src/cmd/mod.rs

@@ -1,3 +1,4 @@
+pub mod estimate;
 pub mod index;
 pub mod merge;
 pub mod superkmer;

src/obikmer2/src/main.rs

@@ -19,6 +19,8 @@ enum Commands {
     Superkmer(cmd::superkmer::SuperkmerArgs),
     /// Merge multiple genome indexes into one
     Merge(cmd::merge::MergeArgs),
+    /// Estimate approximate-evidence false-positive rates for given parameters
+    Estimate(cmd::estimate::EstimateArgs),
 }
 
 fn main() {
@@ -34,5 +36,6 @@ fn main() {
         Commands::Index(args) => cmd::index::run(args),
         Commands::Superkmer(args) => cmd::superkmer::run(args),
         Commands::Merge(args) => cmd::merge::run(args),
+        Commands::Estimate(args) => cmd::estimate::run(args),
     }
 }