feat(dada-pooled): add --gzip for per-sample JSON output (#70)

CHANGELOG.md

@@ -19,6 +19,8 @@ minor versions may carry breaking changes).
 - Experimental **WFA alignment backend** (`--align-backend wfa2`) with a
   `--wfa-max-edits` edit-budget cap (#49, #51). ASV-equivalent to Needleman-
   Wunsch on tested Illumina and PacBio HiFi data, but not byte-identical.
+- `dada-pooled --gzip` writes the per-sample JSON files gzip-compressed as
+  `{sample}.json.gz` (#70).
 - `merge-pairs` records input-file provenance and warns on mismatch (#10).
 - `just` / `make` task runners for build, install, test, and docs (#46).
 

src/cli.rs

@@ -572,6 +572,10 @@ pub enum Commands {
         #[arg(long)]
         compact: bool,
 
+        /// Gzip-compress the per-sample JSON files (written as `{sample}.json.gz`)
+        #[arg(long)]
+        gzip: bool,
+
         /// Print progress to stderr
         #[arg(long)]
         verbose: bool,

src/main.rs

@@ -1238,6 +1238,7 @@ fn main() -> io::Result<()> {
             no_kmer_screen,
             failed_uniques: failed_uniques_path,
             compact,
+            gzip,
             verbose,
         } => {
             use std::collections::{HashMap, HashSet};
@@ -1559,8 +1560,12 @@ fn main() -> io::Result<()> {
 
                 let json = to_json(&Tagged::new("dada-pooled", out), compact)?;
 
-                let path = output_dir.join(format!("{sample_name}.json"));
-                std::fs::write(&path, &json)?;
+                let path = output_dir.join(if gzip {
+                    format!("{sample_name}.json.gz")
+                } else {
+                    format!("{sample_name}.json")
+                });
+                misc::write_maybe_gz(&path, json.as_bytes())?;
                 if verbose {
                     eprintln!(
                         "[dada-pooled] wrote {} ({} ASV(s), {} reads)",