src/obikmer/src/cmd/select/mod.rs

@@ -70,6 +70,17 @@ pub struct SelectArgs {
     /// Overwrite existing output directory
     #[arg(short, long)]
     pub force: bool,
+
+    /// Copy each layer's unchanged kmer-identity files (mphf/unitigs/
+    /// evidence/fingerprint) instead of hard-linking them. By default
+    /// `select` hard-links these (never rewritten by a column
+    /// projection/aggregation, so a hard link is exact and avoids
+    /// transiently doubling disk usage for a large index), falling back to
+    /// a real copy only if linking itself fails (e.g. source and output on
+    /// different filesystems). Set this when the output must survive
+    /// independently of the source on disk.
+    #[arg(long)]
+    pub force_copy: bool,
 }
 
 /// Split a repeatable `<name>:<value>` argument. Exits on malformed input.
@@ -128,6 +139,7 @@ pub fn run(args: SelectArgs) {
     let mut alg = Select::new(&src, &args.output, &specs, output_presence)
         .threshold(args.presence_threshold)
         .force(args.force)
+        .force_copy(args.force_copy)
         .sparse(!args.dense)
         .on_progress(|_: Progress| pb.inc(1));
 

src/obikselect/src/select.rs

@@ -24,6 +24,7 @@ pub struct Select<'a> {
     threshold: u32,
     output_presence: bool,
     force: bool,
+    force_copy: bool,
     sparse: bool,
     reporter: Reporter,
     on_progress: Option<Box<dyn FnMut(Progress) + Send + 'a>>,
@@ -43,6 +44,7 @@ impl<'a> Select<'a> {
             threshold: 0,
             output_presence,
             force: false,
+            force_copy: false,
             sparse: true,
             reporter: Reporter::new(),
             on_progress: None,
@@ -63,6 +65,18 @@ impl<'a> Select<'a> {
         self
     }
 
+    /// Always copy each layer's unchanged kmer-identity files
+    /// (mphf/unitigs/evidence/fingerprint) instead of hard-linking them
+    /// (default: `false` — hard link, falling back to a copy only if
+    /// linking itself fails). Set this when `output` must survive
+    /// independently of `src` on disk — a hard link still shares the same
+    /// underlying inode, so rewriting one path outside `select` would
+    /// affect the other.
+    pub fn force_copy(mut self, v: bool) -> Self {
+        self.force_copy = v;
+        self
+    }
+
     /// Pack the output's presence matrices in the compact sparse format
     /// rather than dense (default: `true`).
     pub fn sparse(mut self, v: bool) -> Self {
@@ -124,7 +138,7 @@ impl Algorithm for Select<'_> {
         runner
             .run(
                 &order,
-                |i| select_partition(&dst, src, i, self.specs, self.threshold, self.output_presence),
+                |i| select_partition(&dst, src, i, self.specs, self.threshold, self.output_presence, self.force_copy),
                 |_, _, _| {
                     done += 1;
                     if let Some(cb) = on_progress.as_mut() {

src/obikselect/src/select_layer.rs

@@ -107,15 +107,26 @@ fn add_result(mb: &mut MatrixBuilder, r: AggResult) -> io::Result<()> {
 
 // ── Helpers ───────────────────────────────────────────────────────────────────
 
-/// Copy all plain files (not subdirectories) from `src_dir` to `dst_dir` —
+/// Carries a layer's kmer identity (mphf/unitigs/evidence/fingerprint) from
-/// carries a layer's kmer identity (mphf/unitigs/evidence/fingerprint)
+/// `src_dir` to `dst_dir` **unchanged** — these files are never rewritten by
-/// across unchanged; only the data matrix (a subdirectory) is rebuilt.
+/// `select` (only the data matrix, a subdirectory, is rebuilt), so a hard
-fn copy_layer_files(src_dir: &Path, dst_dir: &Path) -> io::Result<()> {
+/// link is exact and avoids transiently doubling disk usage for the layer's
+/// largest files on a big index. Falls back to a real copy per file when
+/// linking fails (e.g. `src`/`dst` on different filesystems, `EXDEV`) or
+/// when `force_copy` is set (`--force-copy`, for a destination meant to
+/// survive independently of the source — a hard link still shares the same
+/// underlying inode, so truncating/rewriting one path in place, outside
+/// `select` itself, would affect the other).
+fn copy_layer_files(src_dir: &Path, dst_dir: &Path, force_copy: bool) -> io::Result<()> {
     for entry in fs::read_dir(src_dir)? {
         let entry = entry?;
         let path = entry.path();
-        if path.is_file() {
+        if !path.is_file() {
-            fs::copy(&path, dst_dir.join(entry.file_name()))?;
+            continue;
+        }
+        let dst_path = dst_dir.join(entry.file_name());
+        if force_copy || fs::hard_link(&path, &dst_path).is_err() {
+            fs::copy(&path, &dst_path)?;
         }
     }
     Ok(())
@@ -133,6 +144,7 @@ pub(crate) fn select_partition(
     specs: &[OutputCol],
     threshold: u32,
     output_presence: bool,
+    force_copy: bool,
 ) -> OKIResult<()> {
     let src_partition = src.partition(i)?;
     let dst_partition = dst.partition(i)?;
@@ -147,7 +159,7 @@ pub(crate) fn select_partition(
             .map_err(OKIError::Io)?
             .dir()
             .to_path_buf();
-        copy_layer_files(src_layer.dir(), &dst_layer_dir).map_err(OKIError::Io)?;
+        copy_layer_files(src_layer.dir(), &dst_layer_dir, force_copy).map_err(OKIError::Io)?;
 
         let group_mat: Box<dyn MatrixGroupOps> = match src_layer.content() {
             LayerContent::Count => {