From eaf893174fcb4623a7c0514d9fcc22784b27c1fe Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sun, 26 Apr 2026 14:58:41 +0200
Subject: [PATCH] :recycle: refactor(obikpartitionner): replace low-level I/O
 with obiskio::SKFileWriter

- Replace `limits` module and raw binary I/O with a new high-level abstraction using obiskio::SKFileWriter
- Remove `niffler` dependency and compression logic (Gzip/Zstd/Lz4/Bgzf)
- Simplify PartitionManager to manage partitioned file writers based on kmer hashing
  * Uses `n_partition_bits` for bitmask-based partition selection (2^n partitions)
- Add obiskio as a local dependency
Note: This is likely part of aligning with unified I/O primitives in the obiskio crate.
---
 src/Cargo.lock               |  4 ++++
 src/obikseq/Cargo.toml       |  1 +
 src/obikseq/src/kmer.rs      | 17 +++++++++++++++++
 src/obikseq/src/superkmer.rs | 22 +++++++++++++++++++++-
 4 files changed, 43 insertions(+), 1 deletion(-)

diff --git a/src/Cargo.lock b/src/Cargo.lock
index 8191eed..e6bf410 100644
--- a/src/Cargo.lock
+++ b/src/Cargo.lock
@@ -781,6 +781,9 @@ dependencies = [
 [[package]]
 name = "obikpartitionner"
 version = "0.1.0"
+dependencies = [
+ "obiskio",
+]
 
 [[package]]
 name = "obikrope"
@@ -796,6 +799,7 @@ version = "0.1.0"
 dependencies = [
  "bitvec",
  "criterion2",
+ "xxhash-rust",
 ]
 
 [[package]]
diff --git a/src/obikseq/Cargo.toml b/src/obikseq/Cargo.toml
index bce7f97..daf8193 100644
--- a/src/obikseq/Cargo.toml
+++ b/src/obikseq/Cargo.toml
@@ -5,6 +5,7 @@ edition = "2024"
 
 [dependencies]
 bitvec = "1"
+xxhash-rust = { version = "0.8.15", features = ["xxh3", "const_xxh3"] }
 
 [dev-dependencies]
 criterion2 = { version = "3", features = ["cargo_bench_support"] }
diff --git a/src/obikseq/src/kmer.rs b/src/obikseq/src/kmer.rs
index 32a769e..ad24534 100644
--- a/src/obikseq/src/kmer.rs
+++ b/src/obikseq/src/kmer.rs
@@ -49,6 +49,15 @@ impl std::error::Error for KmerError {}
 #[derive(Debug, Clone, Copy, PartialEq, Eq, PartialOrd, Ord, Hash)]
 pub struct Kmer(u64);
 
+#[inline]
+fn mix64(x: u64) -> u64 {
+    let x = x ^ (x >> 30);
+    let x = x.wrapping_mul(0xbf58476d1ce4e5b9);
+    let x = x ^ (x >> 27);
+    let x = x.wrapping_mul(0x94d049bb133111eb);
+    x ^ (x >> 31)
+}
+
 impl Kmer {
     /// Wrap a raw left-aligned u64 value as a Kmer.
     #[inline]
@@ -144,6 +153,14 @@ impl Kmer {
         let rc = self.revcomp(k);
         if self.0 <= rc.0 { *self } else { rc }
     }
+
+    /// Return a hash of this kmer.
+    ///
+    /// Uses the canonical form of the kmer to compute the hash.
+    #[inline]
+    pub fn hash(&self, k: usize) -> u64 {
+        mix64(self.canonical(k).0)
+    }
 }
 
 // ── tests ─────────────────────────────────────────────────────────────────────
diff --git a/src/obikseq/src/superkmer.rs b/src/obikseq/src/superkmer.rs
index b87ca16..ff27941 100644
--- a/src/obikseq/src/superkmer.rs
+++ b/src/obikseq/src/superkmer.rs
@@ -4,6 +4,7 @@ use crate::encoding::{DEC4, encode_base};
 use crate::kmer::{Kmer, KmerError};
 use crate::revcomp_lookup::REVCOMP4;
 use bitvec::prelude::*;
+use xxhash_rust::xxh3::xxh3_64;
 
 // ── SuperKmerHeader ───────────────────────────────────────────────────────────
 
@@ -312,6 +313,15 @@ impl SuperKmer {
     ///
     /// Returns `true` if already canonical (no change), `false` if revcomp was applied.
     pub fn canonical(&mut self) -> bool {
+        if self.is_canonical() {
+            return true;
+        }
+        self.revcomp();
+        false
+    }
+
+    /// Returns `true` if this super-kmer is in canonical form (lexicographic minimum of forward and revcomp).
+    pub fn is_canonical(&self) -> bool {
         let seql = self.seql();
         for i in 0..seql {
             let fwd = self.nucleotide(i);
@@ -320,12 +330,22 @@ impl SuperKmer {
                 return true;
             }
             if fwd > rev {
-                self.revcomp();
                 return false;
             }
         }
         true
     }
+
+    /// Returns the XXH3 hash of the super-kmer sequence.
+    pub fn hash(&self) -> u64 {
+        if self.is_canonical() {
+            return xxh3_64(&self.seq);
+        } else {
+            let mut rev = self.clone();
+            rev.revcomp();
+            return xxh3_64(&rev.seq);
+        }
+    }
 }
 
 // ── helpers ───────────────────────────────────────────────────────────────────