📖 Update super-kmer theory and implementation to prefer non-degenerate m-mers

- Update super-kmer definition in `kmERS.md` to specify that non-degenerate m-mers are preferred over degenerate ones (degeneracy = homopolymer).
- Refactor `superkmer.rs`: change `.canonical()` to mutate in-place and return bool.
- Add `m` field & canonical-aware minimizer position calculation to SuperKmerIter in obiskbuilder.
- Add helper functions `is_degenerate` and minimizer comparison logic to rolling_stat.rs for consistent tie-breaking.
- Minor formatting cleanup in superkmer command and chunk processing.

docmd/theory/kmers.md

@@ -9,7 +9,7 @@ A **kmer** is a DNA subsequence of fixed length k. Two constraints govern the ch
 
 ## Super-kmers
 
-A **super-kmer** is a maximal run of consecutive kmers from a DNA read, each overlapping the next by k−1 nucleotides. Each kmer of the run carries the same **canonical minimizer**. The **canonical minimizer** of a kmer is the smallest value of `min(m-mer, revcomp(m-mer))` over all m-mers within the kmer (m < k, m odd).
+A **super-kmer** is a maximal run of consecutive kmers from a DNA read, each overlapping the next by k−1 nucleotides. Each kmer of the run carries the same **canonical minimizer**. The **canonical minimizer** of a kmer is the smallest value of `min(m-mer, revcomp(m-mer))` over all m-mers within the kmer (m < k, m odd), with the constraint that **non-degenerate m-mers are always preferred** over degenerate ones. A degenerate m-mer is one composed of a single repeated nucleotide (all-A, all-C, all-G, or all-T); such m-mers are selected only if no non-degenerate candidate exists in the window.
 
 ### Canonical super-kmers
 

src/obikmer/src/cmd/superkmer.rs

@@ -55,8 +55,10 @@ fn detect_format(source: &str, hint: Option<&str>) -> Format {
             _ => Format::Fasta,
         };
     }
-    if source.ends_with(".fq") || source.ends_with(".fastq")
+    if source.ends_with(".fq")
-        || source.ends_with(".fq.gz") || source.ends_with(".fastq.gz")
+        || source.ends_with(".fastq")
+        || source.ends_with(".fq.gz")
+        || source.ends_with(".fastq.gz")
     {
         Format::Fastq
     } else {
@@ -114,22 +116,20 @@ pub fn run(args: SuperkmerArgs) {
             thread::spawn(move || {
                 for raw_chunk in raw_rx {
                     let norm = match format {
-                        Format::Fasta => {
+                        Format::Fasta => obiread::normalize::normalize_fasta_chunk(raw_chunk, k),
-                            obiread::normalize::normalize_fasta_chunk(raw_chunk, k)
+                        Format::Fastq => obiread::normalize::normalize_fastq_chunk(raw_chunk, k),
-                        }
-                        Format::Fastq => {
-                            obiread::normalize::normalize_fastq_chunk(raw_chunk, k)
-                        }
                     };
                     const BATCH_SIZE: usize = 10_000;
                     let mut batch = Vec::with_capacity(BATCH_SIZE);
                     for sk in SuperKmerIter::new(&norm, k, m, level_max, theta) {
                         batch.push(sk);
                         if batch.len() == BATCH_SIZE {
-                            sk_tx.send(std::mem::replace(
+                            sk_tx
-                                &mut batch,
+                                .send(std::mem::replace(
-                                Vec::with_capacity(BATCH_SIZE),
+                                    &mut batch,
-                            )).unwrap();
+                                    Vec::with_capacity(BATCH_SIZE),
+                                ))
+                                .unwrap();
                         }
                     }
                     if !batch.is_empty() {
@@ -151,8 +151,7 @@ pub fn run(args: SuperkmerArgs) {
         for batch in sk_rx {
             for (min_hash, sk) in batch {
                 let partition = (mix64(min_hash) % partitions) as u32;
-                write_scatter(&sk, &mut out, k, m, partition, min_hash)
+                write_scatter(&sk, &mut out, k, m, partition, min_hash).expect("write error");
-                    .expect("write error");
             }
         }
         out.flush().expect("flush error");

src/obikseq/src/superkmer.rs

@@ -286,21 +286,23 @@ impl SuperKmer {
         Ok(self.kmer(i, k)?.canonical(k))
     }
 
-    /// Return this super-kmer in canonical form (lexicographic minimum of forward and revcomp).
+    /// Put this super-kmer in canonical form (lexicographic minimum of forward and revcomp).
-    pub fn canonical(mut self) -> Self {
+    ///
+    /// Returns `true` if already canonical (no change), `false` if revcomp was applied.
+    pub fn canonical(&mut self) -> bool {
         let seql = self.seql();
         for i in 0..seql {
             let fwd = self.nucleotide(i);
             let rev = complement(self.nucleotide(seql - 1 - i));
             if fwd < rev {
-                return self;
+                return true;
             }
             if fwd > rev {
                 self.revcomp();
-                return self;
+                return false;
             }
         }
-        self
+        true
     }
 }
 

src/obiskbuilder/src/iter.rs

@@ -25,6 +25,7 @@ use crate::scratch::SuperKmerScratch;
 pub struct SuperKmerIter<'a> {
     cursor: ForwardCursor<'a>,
     k: usize,
+    m: usize,
     theta: f64,
     scratch: SuperKmerScratch,
     stat: RollingStat,
@@ -43,6 +44,7 @@ impl<'a> SuperKmerIter<'a> {
         Self {
             cursor: rope.fw_cursor(),
             k,
+            m,
             theta,
             scratch: SuperKmerScratch::new(),
             stat: RollingStat::new(k, m, level_max),
@@ -64,7 +66,12 @@ impl<'a> SuperKmerIter<'a> {
         }
         let min = self.prev_min?;
         let mut sk = self.scratch.emit();
-        sk.set_minimizer_pos(self.prev_min_pos as u8);
+        let min_pos = if sk.canonical() {
+            self.prev_min_pos
+        } else {
+            sk.seql() - self.m - self.prev_min_pos
+        };
+        sk.set_minimizer_pos(min_pos as u8);
         Some((min, sk))
     }
 }

src/obiskbuilder/src/rolling_stat.rs

@@ -110,6 +110,19 @@ impl RollingStat {
         sum_f_log_s[ws] += ln_class_size(canonical, ws, false);
     }
 
+    #[inline]
+    fn is_degenerate(canonical: u64, m_mask: u64) -> bool {
+        canonical == 0 || canonical == (0x5555555555555555 & m_mask)
+    }
+
+    #[inline]
+    fn minimizer_worse(existing: u64, candidate: u64, m_mask: u64) -> bool {
+        let ed = Self::is_degenerate(existing, m_mask);
+        let cd = Self::is_degenerate(candidate, m_mask);
+        if ed != cd { return ed; }
+        existing >= candidate
+    }
+
     pub fn push(&mut self, nuc: u8) {
         let bnuc = encode_nuc(nuc);
         let cnuc = bnuc ^ 3;
@@ -132,7 +145,7 @@ impl RollingStat {
                 (self.rolling_k & self.m_mask).min(self.rolling_rck >> ((self.k - self.m) * 2));
             let possible_pos_m = self.received - self.m;
 
-            while self.minimier.back().map_or(false, |it| it.canonical >= possible_canonical_m) {
+            while self.minimier.back().map_or(false, |it| Self::minimizer_worse(it.canonical, possible_canonical_m, self.m_mask)) {
                 self.minimier.pop_back();
             }
             self.minimier