src/obikmer/src/cmd/unitig.rs

@@ -5,7 +5,7 @@ use clap::Args;
 use obidebruinj::GraphDeBruijn;
 use obifastwrite::write_unitig;
 use obikindex::KmerIndex;
-use obisys::{progress_bar, spinner};
+use obisys::{Reporter, Stage, progress_bar, spinner};
 use rayon::prelude::*;
 use tracing::info;
 
@@ -35,9 +35,11 @@ pub fn run(args: UnitigArgs) {
 
     let filters = args.filter.build_filters(&idx.meta().genomes);
     let partition = idx.partition();
+    let mut rep = Reporter::new();
 
     // ── Phase 1 : collect filtered kmers in parallel ──────────────────────────
     let pb = progress_bar("unitig", n as u64, "partitions");
+    let stage = Stage::start("build graph");
     let g = (0..n)
         .into_par_iter()
         .fold(
@@ -57,17 +59,21 @@ pub fn run(args: UnitigArgs) {
         )
         .reduce(GraphDeBruijn::new, |mut a, b| { a.merge(b); a });
     pb.finish_and_clear();
+    rep.push(stage.stop());
 
     info!("unitig: {} distinct k-mers", g.len());
 
     // ── Phase 2 : compute degrees (in-memory, no progress needed) ────────────
+    let stage = Stage::start("compute degrees");
     g.compute_degrees();
+    rep.push(stage.stop());
 
     // ── Phase 3 : enumerate unitigs and write as FASTA ────────────────────────
     let pb = spinner("unitig");
     let stdout = io::stdout();
     let mut out = BufWriter::new(stdout.lock());
 
+    let stage = Stage::start("enumerate unitigs");
     for (j, unitig) in g.iter_unitig().enumerate() {
         write_unitig(&unitig, k, 0, j, &mut out).unwrap_or_else(|e| {
             eprintln!("write error: {e}");
@@ -78,6 +84,8 @@ pub fn run(args: UnitigArgs) {
         }
     }
     pb.finish_and_clear();
+    rep.push(stage.stop());
 
     out.flush().expect("flush error");
+    rep.print();
 }