refactor: improve de Bruijn graph traversal and longtig generation

- Refactored Node representation using compact bitfields for neighbor counts
  and nucleotides; added count_neighbors helper to compute_degrees()
- Introduced StartIter iterator for unitig/longtigu generation with revised
  traversal semantics (e.g., interior node marking)
- Added nucleotide() accessor to Kmer type for 2-bit extraction at position i
- Renamed unitig.rs → longtigs, updated CLI command and output filenames to reflect "long t ig"
- Extended extract_kmers() in scripts/compare.py with duplication statistics
```

scripts/compare_kmers.py

@@ -51,16 +51,21 @@ def iter_sequences(path: str):
         yield header, "".join(parts)
 
 
-def extract_kmers(path: str, k: int) -> set[str]:
-    """Return the set of canonical k-mers from all sequences in *path*."""
-    kmers: set[str] = set()
+def extract_kmers(path: str, k: int) -> tuple[set[str], int]:
+    """Return (set of canonical k-mers, count of duplicated k-mers) from *path*.
+
+    A k-mer is duplicated if its canonical form appears more than once across
+    all sequences in the file.
+    """
+    counts: dict[str, int] = {}
     for _, seq in iter_sequences(path):
-        # skip any character that is not ACGT
         for i in range(len(seq) - k + 1):
             kmer = seq[i : i + k]
             if all(c in "ACGT" for c in kmer):
-                kmers.add(canonical(kmer))
-    return kmers
+                ck = canonical(kmer)
+                counts[ck] = counts.get(ck, 0) + 1
+    duplicated = sum(1 for v in counts.values() if v > 1)
+    return set(counts), duplicated
 
 
 def main():
@@ -81,16 +86,18 @@ def main():
     print()
 
     print("reading A …", file=sys.stderr)
-    set_a = extract_kmers(args.file_a, k)
+    set_a, dup_a = extract_kmers(args.file_a, k)
     print("reading B …", file=sys.stderr)
-    set_b = extract_kmers(args.file_b, k)
+    set_b, dup_b = extract_kmers(args.file_b, k)
 
     only_a = set_a - set_b
     only_b = set_b - set_a
     common = set_a & set_b
 
     print(f"{'kmers in A':<25} {len(set_a):>12,}")
+    print(f"{'duplicated in A':<25} {dup_a:>12,}")
     print(f"{'kmers in B':<25} {len(set_b):>12,}")
+    print(f"{'duplicated in B':<25} {dup_b:>12,}")
     print(f"{'common':<25} {len(common):>12,}")
     print(f"{'only in A (lost)':<25} {len(only_a):>12,}")
     print(f"{'only in B (gained)':<25} {len(only_b):>12,}")