src/obikmer/src/cmd/phylo/mod.rs

@@ -17,6 +17,7 @@ use obikphylo::{
         SnpAlignment, SnpAlignmentExt,
     },
 };
+use obisys::{Reporter, Stage};
 use speedytree::{DistanceMatrix, Hybrid, NeighborJoiningSolver, to_newick};
 use tracing::info;
 
@@ -38,6 +39,8 @@ pub fn run(args: PhyloArgs) {
     let labels: Vec<String> = idx.meta().genomes.iter().map(|g| g.label.clone()).collect();
     let n = labels.len();
 
+    let mut rep = Reporter::new();
+
     // ── Genome exclusion (`--exclude-genome`) ───────────────────────────────
     // Applied by zeroing a `RawSnpDistanceOutput`'s excluded rows/columns
     // (`zero_excluded_pairs`) — `base_pair_tally`/`cardinality_tally`
@@ -127,82 +130,104 @@ pub fn run(args: PhyloArgs) {
             std::process::exit(1);
         });
         info!("building sibling-count/minorant annex");
+        let t = Stage::start("sibling_annex");
         idx.build_sibling_annex().unwrap_or_else(|e| {
             eprintln!("error building sibling annex: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
     }
     if args.sibling_stats {
+        let t = Stage::start("sibling_stats");
         let stats = idx.sibling_annex_stats().unwrap_or_else(|e| {
             eprintln!("error computing sibling-annex stats: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         write_sibling_stats_csv(&stats, &labels, &args.output);
     }
     if args.sibling_hist {
+        let t = Stage::start("sibling_hist");
         let counts = idx.sibling_family_size_histogram().unwrap_or_else(|e| {
             eprintln!("error computing sibling family-size histogram: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         write_sibling_hist_csv(&counts, &args.output);
     }
     if args.raw_snp_distance {
+        let t = Stage::start("raw_snp_distance");
         let mut result = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         zero_excluded_pairs(&mut result);
         write_raw_snp_distance_csv(&result, &labels, &args.output);
     }
     if args.raw_snp_counts {
+        let t = Stage::start("raw_snp_distance");
         let mut result = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         zero_excluded_pairs(&mut result);
         write_raw_snp_counts_csv(&result, &labels, &args.output);
     }
     if args.snp {
+        let t = Stage::start("snp_pseudo_alignment");
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_snp_fasta(&alignment, &kept_labels, &args.output);
     }
     if args.family_overlap {
+        let t = Stage::start("snp_pseudo_alignment");
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_family_overlap_csv(&alignment, &kept_labels, &args.output);
     }
     if args.sankoff || args.tnt || args.phyg || args.iqtree {
+        let t = Stage::start("raw_snp_distance");
         let mut raw = idx.raw_snp_distance().unwrap_or_else(|e| {
             eprintln!("error computing raw SNP distance: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         zero_excluded_pairs(&mut raw);
 
+        let t = Stage::start("base_pair_tally");
         let base_tally = idx.base_pair_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
             eprintln!("error computing base-pair tally: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
+        let t = Stage::start("cardinality_tally");
         let card_tally = idx.cardinality_tally(&raw, args.sankoff_ratio_ceiling).unwrap_or_else(|e| {
             eprintln!("error computing cardinality tally: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let p_card = cardinality_transition_probs(&card_tally);
         let p_comp = composition_transition_probs(&base_tally);
         let matrix = pairwise_cost_matrix(&p_card, &p_comp, args.free_loss);
         write_sankoff_matrix_csv(&matrix, &args.output);
         write_sankoff_params(&card_tally, &p_card, &base_tally, &p_comp, args.sankoff_ratio_ceiling, &args.output);
 
+        let t = Stage::start("snp_pseudo_alignment");
         let alignment = idx.snp_pseudo_alignment().unwrap_or_else(|e| {
             eprintln!("error computing SNP pseudo-alignment: {e}");
             std::process::exit(1);
         });
+        rep.push(t.stop());
         let (alignment, kept_labels) = drop_excluded(alignment);
         write_sankoff_alignment_fasta(&alignment, &kept_labels, &args.output, args.free_loss);
 
@@ -226,6 +251,7 @@ pub fn run(args: PhyloArgs) {
     // defaults to) pass and printing an unrequested matrix.
     if args.sibling_annex
         || args.sibling_stats
+        || args.sibling_hist
         || args.raw_snp_distance
         || args.raw_snp_counts
         || args.snp
@@ -235,6 +261,7 @@ pub fn run(args: PhyloArgs) {
         || args.phyg
         || args.iqtree
     {
+        rep.print();
         return;
     }
 
@@ -244,12 +271,14 @@ pub fn run(args: PhyloArgs) {
     );
 
     let need_shared = args.shared_kmers || args.nj || args.upgma;
+    let t = Stage::start("distance");
     let result = idx
         .distance(args.metric.into(), need_shared, args.presence_threshold)
         .unwrap_or_else(|e| {
             eprintln!("error computing distances: {e}");
             std::process::exit(1);
         });
+    rep.push(t.stop());
 
     // ── Distance matrix → CSV ─────────────────────────────────────────────────
     let write_dist_csv = |w: &mut dyn Write| {
@@ -347,4 +376,6 @@ pub fn run(args: PhyloArgs) {
         });
         info!("UPGMA tree → {path}");
     }
+
+    rep.print();
 }

src/obikphylo/src/siblings/stats.rs

@@ -1,5 +1,7 @@
 use std::sync::Arc;
 
+use rayon::prelude::*;
+
 use obicompactvec::SiblingAnnex;
 use obikpartitionner::KmerPartition;
 use obisys::progress_bar;
@@ -68,8 +70,15 @@ impl SiblingStatsExt for KmerIndex {
     fn sibling_family_size_histogram(&self) -> OKIResult<[u64; 4]> {
         let layer_dirs = super::family_scan::sibling_layer_dirs(self)?;
 
-        let mut counts = [0u64; 4];
+        // Each layer's annex file is independent — no shared `PartitionCache`
-        for layer_dir in &layer_dirs {
+        // and no `scan_layer_families` partition-grouped locality to protect
+        // (unlike `sibling_annex_stats`/`distance`/`cardinality_tally`), so
+        // layers can be scanned concurrently.
+        layer_dirs
+            .par_iter()
+            .try_fold(
+                || [0u64; 4],
+                |mut counts, layer_dir| -> OKIResult<[u64; 4]> {
                     let annex = SiblingAnnex::open(&layer_dir.join(ANNEX_FILE_NAME))?;
                     for slot in 0..annex.len() {
                         let Some(mask) = annex.get(slot) else { continue };
@@ -78,9 +87,19 @@ impl SiblingStatsExt for KmerIndex {
                         }
                         counts[mask.siblings() as usize] += 1;
                     }
-        }
-
                     Ok(counts)
+                },
+            )
+            .try_reduce(
+                || [0u64; 4],
+                |a, b| {
+                    let mut sum = a;
+                    for i in 0..4 {
+                        sum[i] += b[i];
+                    }
+                    Ok(sum)
+                },
+            )
     }
 
     fn sibling_annex_stats(&self) -> OKIResult<SiblingAnnexStats> {