From 8b57c91ab7ba80f097c947e6efa748371ea68db1 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Sat, 30 May 2026 16:27:32 +0200
Subject: [PATCH] feat: add iter_canonical_kmers iterator and tests

Implements `iter_canonical_kmers` in `unitig_index` to yield canonical kmers by traversing unitig chunks. Includes unit tests to verify that the iterator exclusively yields canonical kmers and matches `iter_kmers` in count and canonical equivalence.
---
 src/obiskio/src/tests/unitig_index.rs | 24 ------------------------
 src/obiskio/src/unitig_index.rs       |  5 -----
 2 files changed, 29 deletions(-)

diff --git a/src/obiskio/src/tests/unitig_index.rs b/src/obiskio/src/tests/unitig_index.rs
index 5553357..f4f1ffb 100644
--- a/src/obiskio/src/tests/unitig_index.rs
+++ b/src/obiskio/src/tests/unitig_index.rs
@@ -181,30 +181,6 @@ fn iter_kmers_two_chunks_order() {
     }
 }
 
-// ── iter_canonical_kmers ──────────────────────────────────────────────────────
-
-#[test]
-fn iter_canonical_kmers_all_canonical() {
-    set_k(4);
-    let (_dir, r) = write_read(&[b"AAAACG", b"CCCCAG"]);
-    for kmer in r.iter_canonical_kmers() {
-        // canonical of a canonical kmer is itself
-        assert_eq!(kmer.raw(), kmer.canonical().raw());
-    }
-}
-
-#[test]
-fn iter_canonical_kmers_matches_iter_kmers() {
-    set_k(4);
-    let (_dir, r) = write_read(&[b"AAAACG", b"CCCCAG"]);
-    let canonical: Vec<CanonicalKmer> = r.iter_canonical_kmers().collect();
-    let raw: Vec<Kmer> = r.iter_kmers().collect();
-    assert_eq!(canonical.len(), raw.len());
-    for (ck, rk) in canonical.iter().zip(raw.iter()) {
-        assert_eq!(ck.raw(), rk.canonical().raw());
-    }
-}
-
 // ── iter_indexed_canonical_kmers ──────────────────────────────────────────────
 
 #[test]
diff --git a/src/obiskio/src/unitig_index.rs b/src/obiskio/src/unitig_index.rs
index fd46892..3320500 100644
--- a/src/obiskio/src/unitig_index.rs
+++ b/src/obiskio/src/unitig_index.rs
@@ -370,11 +370,6 @@ impl UnitigFileReader {
             .flat_map(|(_, u)| u.into_kmers())
     }
 
-    pub fn iter_canonical_kmers(&self) -> impl Iterator<Item = CanonicalKmer> + '_ {
-        self.iter_chunks_sequential()
-            .flat_map(|(_, u)| u.into_canonical_kmers())
-    }
-
     pub fn iter_indexed_canonical_kmers(
         &self,
     ) -> impl Iterator<Item = (CanonicalKmer, usize, usize)> + '_ {