docmd/architecture/query.md

@@ -153,7 +153,7 @@ Genome keys follow the iteration order of `meta.genomes`.
 |---|---|---|---|
 | `kmer_count` | int | always | k-mers confirmed (post-Findere) with at least one genome match |
 | `kmer_missing` | int | `--count-missing` | k-mers absent from the index entirely (pre-Findere None) |
-| `kmer_strict_matches` | object | always | per-genome accumulated value (label → count or 0/1) |
+| `kmer_strict_matches` | object | always | per-genome accumulated value, non-zero entries only (label → count or 0/1) |
 | `coverage` | object | `--detail` | per-genome array of per-position contributions (label → [u32]) |
 
 `kmer_count + kmer_missing` ≤ total k_user-mers in the sequence. The gap corresponds to k_user-mers whose z-window was not fully confirmed (at least one s-mer absent or zero for all genomes) but whose first s-mer was present in the index.

src/Cargo.lock

@@ -1704,7 +1704,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.35"
+version = "1.1.36"
 dependencies = [
  "clap",
  "csv",

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.35"
+version = "1.1.36"
 edition = "2024"
 
 [[bin]]

src/obikmer/src/cmd/query.rs

@@ -501,7 +501,9 @@ fn emit_batch(
 
         let mut match_map = serde_json::Map::new();
         for (g, genome) in meta.genomes.iter().enumerate() {
-            match_map.insert(genome.label.clone(), acc.genome_totals[g].into());
+            if acc.genome_totals[g] != 0 {
+                match_map.insert(genome.label.clone(), acc.genome_totals[g].into());
+            }
         }
         ann.insert("kmer_strict_matches".into(), match_map.into());