src/obikmer/src/steps/scatter.rs

@@ -95,10 +95,13 @@ pub fn scatter(
     let mut ema_rate: f64 = 0.0;
     let mut last_t = Instant::now();
     let mut last_bases: u64 = 0;
+    let kmer_overlap = (k - 1) as u64;
     const ALPHA: f64 = 0.15;
 
     for batch in pipe.apply(throttled, n_workers, 1) {
-        total_bases += batch.iter().map(|sk| sk.seql() as u64).sum::<u64>();
+        total_bases += batch.iter()
+            .map(|sk| (sk.seql() as u64).saturating_sub(kmer_overlap))
+            .sum::<u64>();
         let now = Instant::now();
         let dt = now.duration_since(last_t).as_secs_f64();
         if dt > 0.1 {