src/obikmer/src/cli.rs

@@ -10,8 +10,9 @@ use obikseq::RoutableSuperKmer;
 
 #[derive(Args)]
 pub struct CommonArgs {
-    /// Input files or directories (FASTA/FASTQ, optionally gzip-compressed)
-    #[arg(num_args = 1..)]
+    /// Input files or directories (FASTA/FASTQ, optionally gzip-compressed).
+    /// If omitted, reads from stdin.
+    #[arg(num_args = 0..)]
     pub inputs: Vec<String>,
 
     /// k-mer size
@@ -63,7 +64,11 @@ pub fn block_size_to_bits(n: usize) -> u8 {
 
 impl CommonArgs {
     pub fn seqfile_paths(&self) -> obiread::PathIter {
-        let paths = self.inputs.iter().map(PathBuf::from).collect();
+        let paths: Vec<PathBuf> = if self.inputs.is_empty() {
+            vec![PathBuf::from("-")]
+        } else {
+            self.inputs.iter().map(PathBuf::from).collect()
+        };
         obiread::PathIter::new(paths)
     }
 }

src/obiread/src/path_iterator.rs

@@ -19,12 +19,13 @@ impl PathIter {
             file_buffer: Vec::new(),
         };
         for path in paths {
+            // "-" is the stdin sentinel — pass it through without any extension
+            // check or directory expansion.
+            if path.as_os_str() == "-" {
+                iter.file_buffer.push(path);
+            } else if is_fasta_or_fastq(&path) {
                 // Avoid stat() at construction time on network filesystems (Lustre, NFS)
                 // where metadata operations can be 100s of milliseconds each.
-            // Paths that look like sequence files are assumed to be files.
-            // Anything else is treated as a potential directory and expanded lazily
-            // in next(); read_dir errors are silently skipped.
-            if is_fasta_or_fastq(&path) {
                 iter.file_buffer.push(path);
             } else {
                 iter.dir_stack.push(path);