From bba5147f0faf159a015e63b464eb77c55cb9939a Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric@coissac.eu>
Date: Wed, 3 Jun 2026 15:10:15 +0200
Subject: [PATCH] fix: account for k-mer overlap in total_bases calculation

Introduces a `kmer_overlap` variable (`k-1`) and modifies the `total_bases` accumulation to subtract this overlap from each sequence's length. This ensures the base count accurately reflects only valid k-mer starting positions rather than raw sequence length.
---
 src/obikmer/src/steps/scatter.rs | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/obikmer/src/steps/scatter.rs b/src/obikmer/src/steps/scatter.rs
index 80d789e..cb5a14b 100644
--- a/src/obikmer/src/steps/scatter.rs
+++ b/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 {