📖 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.

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