docmd/index.md

@@ -17,7 +17,7 @@
 | `unitig`    | Dump unitigs from a built index to stdout (debug) |
 | `estimate`  | Estimate approximate-index parameters (z, evidence bits, FP rates) before indexing |
 | `reindex`   | Convert an index's evidence in-place: exact ↔ approx |
-| `utils`     | Miscellaneous index utilities: `--new-label NEW=OLD` renames a genome label in-place |
+| `utils`     | Miscellaneous index utilities: `--new-label NEW=OLD` renames a genome label in-place (NEW gets OLD's identity) |
 
 ## Constraints
 
@@ -27,6 +27,20 @@
 - Canonical form: `min(kmer, revcomp(kmer))` reduces strand-symmetric space by half
 - Input formats: FASTA, FASTQ, gzip, streaming stdin; `index` reads from stdin automatically when no input files are provided (`-` can also be passed explicitly among other paths)
 
+## Genome label constraints
+
+Genome labels are arbitrary Unicode strings with the following restrictions:
+
+| Character | Forbidden | Reason |
+|-----------|-----------|--------|
+| `/` | yes | filesystem path separator |
+| `=` | yes | `--new-label` parser separator |
+| `\0` | yes | null byte |
+| `\n` `\r` `\t` | yes | break CSV output |
+| spaces | **allowed** | use shell quoting: `--new-label 'new label=old label'` |
+
+Empty labels are also rejected. Labels derived automatically from the index directory name (when `--label` is omitted) are not validated since they come from the filesystem and are already safe.
+
 ## Priority operations
 
 - Kmer counting (frequencies)

src/obikmer/src/cmd/query.rs

@@ -59,8 +59,8 @@ pub struct SKDesc {
     /// Index of the source sequence within the batch.
     pub seq_idx: u32,
     /// Kmer offset of the first kmer of this superkmer within its sequence.
-    /// Computed as the cumulative number of kmers emitted before this superkmer
+    /// Reserved for `--detail` coverage vectors (not yet consumed).
-    /// in the same sequence. Used for `--detail` coverage vectors.
+    #[allow(dead_code)]
     pub kmer_offset: u32,
 }
 
@@ -76,7 +76,8 @@ pub struct QueryBatch {
     pub ids: Vec<String>,
     /// Raw sequence bytes (for output), in batch order.
     pub seqs: Vec<Vec<u8>>,
-    /// Per-sequence total kmer count (kmer_count + kmer_missing).
+    /// Per-sequence total kmer count. Reserved for `--detail` (not yet consumed).
+    #[allow(dead_code)]
     pub n_kmers: Vec<u32>,
     /// Deduplicated superkmer map.
     pub map: HashMap<RoutableSuperKmer, Vec<SKDesc>>,

src/obiskbuilder/src/rolling_stat.rs

@@ -24,10 +24,6 @@ impl<T: Copy + Default, const N: usize> Ring<T, N> {
         }
     }
     #[inline]
-    fn is_empty(&self) -> bool {
-        self.len == 0
-    }
-    #[inline]
     fn clear(&mut self) {
         self.len = 0;
         self.head = 0;
@@ -67,10 +63,6 @@ impl<T: Copy + Default, const N: usize> Ring<T, N> {
         }
     }
 
-    /// Iterate over elements front-to-back (copies, since T: Copy).
-    fn iter(&self) -> impl Iterator<Item = T> + '_ {
-        (0..self.len).map(move |i| self.buf[(self.head + i) % N])
-    }
 }
 
 // ── MmerItem ──────────────────────────────────────────────────────────────────