docmd/index.md

@@ -17,6 +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 |
 
 ## Constraints
 
@@ -24,7 +25,7 @@
 - Maximum efficiency in computation, memory, and disk usage
 - k odd, k ∈ [11, 31], fixed at runtime; kmer fits in a u64 (2 bits/base)
 - Canonical form: `min(kmer, revcomp(kmer))` reduces strand-symmetric space by half
-- Input formats: FASTA, FASTQ, gzip, streaming stdin
+- 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)
 
 ## Priority operations
 

src/obikindex/src/lib.rs

@@ -12,5 +12,5 @@ pub use error::{OKIError, OKIResult};
 pub use distance::{DistanceMetric, DistanceOutput};
 pub use index::KmerIndex;
 pub use merge::MergeMode;
-pub use meta::{GenomeInfo, IndexConfig, IndexMeta, META_FILENAME};
+pub use meta::{validate_label, GenomeInfo, IndexConfig, IndexMeta, META_FILENAME};
 pub use state::{IndexState, SENTINEL_COUNTED, SENTINEL_INDEXED, SENTINEL_SCATTERED};

src/obikindex/src/meta.rs

@@ -70,3 +70,26 @@ impl IndexMeta {
         self.genomes.iter().map(|g| g.label.as_str())
     }
 }
+
+/// Validate a user-supplied genome label.
+///
+/// Forbidden: `/` (filesystem separator), `=` (--new-label parser separator),
+/// `\0` (null byte), `\n`, `\r`, `\t` (break CSV output).
+/// Empty labels are also rejected.
+pub fn validate_label(label: &str) -> Result<(), String> {
+    if label.is_empty() {
+        return Err("genome label must not be empty".into());
+    }
+    const FORBIDDEN: &[char] = &['/', '=', '\0', '\n', '\r', '\t'];
+    if let Some(c) = label.chars().find(|c| FORBIDDEN.contains(c)) {
+        let display = match c {
+            '\0' => "\\0 (null)".to_string(),
+            '\n' => "\\n (newline)".to_string(),
+            '\r' => "\\r (carriage return)".to_string(),
+            '\t' => "\\t (tab)".to_string(),
+            c    => format!("'{c}'"),
+        };
+        return Err(format!("genome label contains forbidden character {display}"));
+    }
+    Ok(())
+}

src/obikmer/src/cmd/index.rs

@@ -1,7 +1,7 @@
 use std::path::PathBuf;
 
 use clap::Args;
-use obikindex::{GenomeInfo, IndexConfig, IndexState, KmerIndex};
+use obikindex::{validate_label, GenomeInfo, IndexConfig, IndexState, KmerIndex};
 use obilayeredmap::IndexMode;
 
 fn parse_key_value(s: &str) -> Result<(String, String), String> {
@@ -194,6 +194,10 @@ pub fn run(args: IndexArgs) {
             block_bits,
         };
         let genome_info = args.label.as_ref().map(|label| {
+            validate_label(label).unwrap_or_else(|e| {
+                eprintln!("error: --label: {e}");
+                std::process::exit(1);
+            });
             let mut info = GenomeInfo::new(label.clone());
             for (k, v) in &args.meta {
                 info.meta.insert(k.clone(), v.clone());

src/obikmer/src/cmd/mod.rs

@@ -1,4 +1,5 @@
 pub mod annotate;
+pub mod utils;
 pub mod distance;
 pub mod dump;
 pub mod estimate;

src/obikmer/src/cmd/utils.rs

@@ -0,0 +1,91 @@
+use std::path::PathBuf;
+
+use clap::Args;
+use obikindex::{validate_label, KmerIndex};
+use tracing::info;
+
+#[derive(Args)]
+pub struct UtilsArgs {
+    /// Index directory to operate on
+    pub index: PathBuf,
+
+    /// Set a new genome label: NEW_LABEL=OLD_LABEL
+    #[arg(long, value_name = "NEW=OLD")]
+    pub new_label: Option<String>,
+}
+
+pub fn run(args: UtilsArgs) {
+    let mut any = false;
+
+    if let Some(spec) = &args.new_label {
+        any = true;
+        run_rename(&args.index, spec);
+    }
+
+    if !any {
+        eprintln!("utils: no operation specified. Available options: --new-label NEW=OLD");
+        std::process::exit(1);
+    }
+}
+
+fn run_rename(index_path: &PathBuf, spec: &str) {
+    let (old_label, new_label) = parse_rename_spec(spec);
+
+    let mut idx = KmerIndex::open(index_path).unwrap_or_else(|e| {
+        eprintln!("error opening index: {e}");
+        std::process::exit(1);
+    });
+
+    let pos = idx
+        .meta()
+        .genomes
+        .iter()
+        .position(|g| g.label == old_label)
+        .unwrap_or_else(|| {
+            eprintln!("error: genome '{old_label}' not found in index");
+            std::process::exit(1);
+        });
+
+    validate_label(&new_label).unwrap_or_else(|e| {
+        eprintln!("error: --new-label: {e}");
+        std::process::exit(1);
+    });
+
+    // Check the new label is not already taken.
+    if idx.meta().genomes.iter().any(|g| g.label == new_label) {
+        eprintln!("error: label '{new_label}' already exists in index");
+        std::process::exit(1);
+    }
+
+    idx.meta_mut().genomes[pos].label = new_label.clone();
+    idx.meta_mut().write(index_path).unwrap_or_else(|e| {
+        eprintln!("error writing index metadata: {e}");
+        std::process::exit(1);
+    });
+
+    // Rename the spectrum file if it exists.
+    let spectrums_dir = index_path.join("spectrums");
+    let old_spectrum = spectrums_dir.join(format!("{old_label}.json"));
+    let new_spectrum = spectrums_dir.join(format!("{new_label}.json"));
+    if old_spectrum.exists() {
+        std::fs::rename(&old_spectrum, &new_spectrum).unwrap_or_else(|e| {
+            eprintln!("warning: could not rename spectrum file: {e}");
+        });
+    }
+
+    info!("renamed genome '{old_label}' → '{new_label}'");
+}
+
+fn parse_rename_spec(spec: &str) -> (String, String) {
+    let eq = spec.find('=').unwrap_or_else(|| {
+        eprintln!("error: --new-label expects NEW_LABEL=OLD_LABEL, got '{spec}'");
+        std::process::exit(1);
+    });
+    let new = spec[..eq].trim().to_string();
+    let old = spec[eq + 1..].trim().to_string();
+    if old.is_empty() || new.is_empty() {
+        eprintln!("error: --new-label: both old and new labels must be non-empty");
+        std::process::exit(1);
+    }
+    (old, new)
+}

src/obikmer/src/main.rs

@@ -36,6 +36,8 @@ enum Commands {
     Estimate(cmd::estimate::EstimateArgs),
     /// Convert an index's evidence in-place: exact ↔ approx
     Reindex(cmd::reindex::ReindexArgs),
+    /// Miscellaneous index utilities (--rename, …)
+    Utils(cmd::utils::UtilsArgs),
 }
 
 fn main() {
@@ -68,6 +70,7 @@ fn main() {
         Commands::Unitig(args)    => cmd::unitig::run(args),
         Commands::Estimate(args)  => cmd::estimate::run(args),
         Commands::Reindex(args)   => cmd::reindex::run(args),
+        Commands::Utils(args)     => cmd::utils::run(args),
     }
 
     #[cfg(feature = "profiling")]