feat: support exact and approximate evidence in layer construction

Refactored `MphfLayer::build` to accept an `EvidenceKind` parameter, routing to exact (index-based, parallel MPHF, writes `evidence.bin`) or approximate (sequential mmap iterator, writes `fingerprint.bin`) pipelines. Introduced `CanonicalKmerIter` for memory-mapped, chunked k-mer iteration with O(1) resets via `Arc<Mmap>`. Updated layer and map APIs to forward evidence kind, added `push_layer` for count matrices, and adjusted tests and public exports accordingly.

src/obiskio/src/lib.rs

@@ -8,7 +8,8 @@ pub use error::{SKError, SKResult};
 pub use meta::SKFileMeta;
 pub use pool::{SKFilePool, SKFileWriter, SharedPool, create_token, create_token_with};
 pub use reader::{SKFileIter, SKFileReader};
-pub use unitig_index::{UnitigFileReader, UnitigFileWriter, build_unitig_idx, DEFAULT_BLOCK_BITS};
+pub use unitig_index::{UnitigFileReader, UnitigFileWriter, build_unitig_idx, DEFAULT_BLOCK_BITS,
+                       CanonicalKmerIter};
 
 use std::path::{Path, PathBuf};
 

src/obiskio/src/unitig_index.rs

@@ -1,6 +1,7 @@
 use std::fs::File;
 use std::io::{BufWriter, Write as _};
 use std::path::{Path, PathBuf};
+use std::sync::Arc;
 
 use memmap2::Mmap;
 use obikseq::{CanonicalKmer, Kmer, Unitig};
@@ -439,6 +440,85 @@ fn extract_kmer_raw(bytes: &[u8], j: usize, k: usize) -> u64 {
     raw << (64 - 2 * k)
 }
 
+// ── CanonicalKmerRawIter ──────────────────────────────────────────────────────
+
+// ── CanonicalKmerIter ─────────────────────────────────────────────────────────
+
+/// Sequential iterator over [`CanonicalKmer`] from a `unitigs.bin` file.
+///
+/// Holds an `Arc<Mmap>` so that `Clone` is O(1): both copies share the same
+/// memory-mapped pages.  Cloning resets the cursor to position 0 — this lets
+/// ptr_hash's `new_from_par_iter` (which requires a `Clone`-able parallel
+/// iterator via `par_bridge()`) make multiple passes without ever creating
+/// a `.idx` file.
+pub struct CanonicalKmerIter {
+    mmap:      Arc<Mmap>,
+    k:         usize,
+    chunk_pos: usize,   // byte offset of the current chunk header
+    data_pos:  usize,   // byte offset of the current chunk's sequence bytes
+    n_kmers:   usize,   // kmers in current chunk
+    kmer_idx:  usize,   // next kmer index to yield within the current chunk
+}
+
+impl CanonicalKmerIter {
+    pub fn new(path: &Path) -> SKResult<Self> {
+        let file = File::open(path).map_err(SKError::Io)?;
+        let mmap = Arc::new(unsafe { Mmap::map(&file).map_err(SKError::Io)? });
+        let k = obikseq::params::k();
+        let mut s = Self { mmap, k, chunk_pos: 0, data_pos: 0, n_kmers: 0, kmer_idx: 0 };
+        s.load_chunk();
+        Ok(s)
+    }
+
+    #[inline]
+    fn load_chunk(&mut self) {
+        if self.chunk_pos < self.mmap.len() {
+            let seql_minus_k = self.mmap[self.chunk_pos] as usize;
+            self.n_kmers  = seql_minus_k + 1;
+            self.data_pos = self.chunk_pos + 1;
+            self.kmer_idx = 0;
+        }
+    }
+}
+
+impl Clone for CanonicalKmerIter {
+    fn clone(&self) -> Self {
+        let mut c = Self {
+            mmap:      Arc::clone(&self.mmap),
+            k:         self.k,
+            chunk_pos: 0,
+            data_pos:  0,
+            n_kmers:   0,
+            kmer_idx:  0,
+        };
+        c.load_chunk();
+        c
+    }
+}
+
+impl Iterator for CanonicalKmerIter {
+    type Item = CanonicalKmer;
+
+    #[inline]
+    fn next(&mut self) -> Option<CanonicalKmer> {
+        loop {
+            if self.chunk_pos >= self.mmap.len() {
+                return None;
+            }
+            if self.kmer_idx < self.n_kmers {
+                let raw   = extract_kmer_raw(&self.mmap[self.data_pos..], self.kmer_idx, self.k);
+                let canon = canonical_raw(raw, self.k);
+                self.kmer_idx += 1;
+                return Some(CanonicalKmer::from_raw_unchecked(canon));
+            }
+            let seql_minus_k = self.mmap[self.chunk_pos] as usize;
+            let byte_len     = (seql_minus_k + self.k + 3) / 4;
+            self.chunk_pos  += 1 + byte_len;
+            self.load_chunk();
+        }
+    }
+}
+
 #[cfg(test)]
 #[path = "tests/unitig_index.rs"]
 mod tests;