feat: add seq_hash() and refactor canonical hashing

Introduce `. seqhash(&self)` for direct XXH3-64 sequencing of packed bytes, and remove legacy `.hash()` method that used conditional canonicalization via revcomp. Also update partitioning logic to use `sk.hashseq_hash()` and deduplicate imports.

src/obikmer/src/cmd/superkmer.rs

@@ -25,7 +25,7 @@ fn write_batch(
     let partition_mask = (1u64 << partition_bits) - 1;
     for rsk in batch {
         let minimizer = *rsk.minimizer();
-        let partition = (minimizer.hash(m) & partition_mask) as usize;
+        let partition = (minimizer.seq_hash(m) & partition_mask) as usize;
         write_scatter(rsk.superkmer(), out, k, m, partition, minimizer)?;
     }
     Ok(())

src/obikpartitionner/src/partition.rs

@@ -14,8 +14,8 @@ use remove_dir_all::remove_dir_all;
 
 use niffler::Level;
 use niffler::send::compression::Format;
-use obikseq::superkmer::SuperKmer;
 use obikseq::RoutableSuperKmer;
+use obikseq::superkmer::SuperKmer;
 use obiskio::{SKFileMeta, SKFileReader, SKFileWriter, SKResult};
 use rayon::prelude::*;
 use serde::{Deserialize, Serialize};
@@ -124,7 +124,8 @@ impl KmerPartition {
     /// Route and write one super-kmer to its partition file.
     pub fn write(&mut self, rsk: RoutableSuperKmer) -> SKResult<()> {
         self.check_not_closed()?;
-        let partition = (rsk.minimizer().hash(self.minimizer_size) & self.partitions_mask) as usize;
+        let partition =
+            (rsk.minimizer().seq_hash(self.minimizer_size) & self.partitions_mask) as usize;
         let sk = rsk.into_superkmer();
         self.ensure_writer(partition)?.write(&sk)
     }
@@ -133,7 +134,8 @@ impl KmerPartition {
     pub fn write_batch(&mut self, rsks: Vec<RoutableSuperKmer>) -> SKResult<()> {
         self.check_not_closed()?;
         for rsk in rsks {
-            let partition = (rsk.minimizer().hash(self.minimizer_size) & self.partitions_mask) as usize;
+            let partition =
+                (rsk.minimizer().seq_hash(self.minimizer_size) & self.partitions_mask) as usize;
             let sk = rsk.into_superkmer();
             self.ensure_writer(partition)?.write(&sk)?;
         }
@@ -441,9 +443,8 @@ fn dereplicate_partition(dir: &Path, level: Level, n_temp: usize, k: usize) -> S
                 .collect::<SKResult<_>>()?;
 
             let mut reader = SKFileReader::open(&raw_path, k)?;
-            while let Some(mut sk) = reader.read()? {
+            while let Some(sk) = reader.read()? {
-                sk.canonical();
+                let bucket = (sk.seq_hash() & temp_mask) as usize;
-                let bucket = (sk.hash() & temp_mask) as usize;
                 writers[bucket].write(&sk)?;
             }
             for w in &mut writers {
@@ -473,8 +474,7 @@ fn load_bucket(path: &Path, k: usize) -> SKResult<HashMap<SuperKmer, u64>> {
         .unwrap_or(0);
     let mut map: HashMap<SuperKmer, u64> = HashMap::with_capacity(capacity);
     let mut reader = SKFileReader::open(path, k)?;
-    while let Some(mut sk) = reader.read()? {
+    while let Some(sk) = reader.read()? {
-        sk.canonical();
         let count = sk.count() as u64;
         *map.entry(sk).or_insert(0) += count;
     }

src/obikseq/src/kmer.rs

@@ -160,7 +160,7 @@ impl Kmer {
     ///
     /// Uses the canonical form of the kmer to compute the hash.
     #[inline]
-    pub fn hash(&self, k: usize) -> u64 {
+    pub fn seq_hash(&self, k: usize) -> u64 {
         mix64(self.canonical(k).0)
     }
 

src/obikseq/src/sequence.rs

@@ -1,5 +1,5 @@
 pub trait Sequence {
-    fn len(&self) -> usize;
     fn sequence(&self) -> &[u8];
-    fn revcomp(&self) -> Self;
+    fn canonical(&self) -> Self;
+    fn seq_hash(&self) -> u64;
 }

src/obikseq/src/superkmer.rs

@@ -155,7 +155,9 @@ impl SuperKmer {
     }
 
     /// Reverse-complement this super-kmer in place.
-    pub fn revcomp(&mut self) {
+    ///
+    /// This method is only used internally by the build method.
+    fn revcomp(&mut self) {
         let seql = self.len();
         let n = byte_len(seql);
 
@@ -280,7 +282,7 @@ impl SuperKmer {
     /// Put this super-kmer in canonical form (lexicographic minimum of forward and revcomp).
     ///
     /// Returns `true` if already canonical (no change), `false` if revcomp was applied.
-    pub fn canonical(&mut self) -> bool {
+    fn canonical(&mut self) -> bool {
         if self.is_canonical() {
             return true;
         }
@@ -289,7 +291,7 @@ impl SuperKmer {
     }
 
     /// Returns `true` if this super-kmer is in canonical form (lexicographic minimum of forward and revcomp).
-    pub fn is_canonical(&self) -> bool {
+    fn is_canonical(&self) -> bool {
         let seql = self.len();
         for i in 0..seql {
             let fwd = self.nucleotide(i);
@@ -314,15 +316,9 @@ impl SuperKmer {
         self.iter_kmers(k).map(move |km| km.canonical(k))
     }
 
-    /// Returns the XXH3 hash of the super-kmer sequence.
+    /// Returns the XXH3-64 hash of the packed sequence bytes.
-    pub fn hash(&self) -> u64 {
+    pub fn seq_hash(&self) -> u64 {
-        if self.is_canonical() {
+        xxh3_64(&self.seq)
-            return xxh3_64(&self.seq);
-        } else {
-            let mut rev = self.clone();
-            rev.revcomp();
-            return xxh3_64(&rev.seq);
-        }
     }
 }