fix(bitmatrix): explicitly compute diagonal entries for self-similarity

The pairwise matrix functions now explicitly calculate and overwrite diagonal entries using `f(i,i)`, replacing previous implicit symmetric mirroring or default values. Documentation has been updated to clarify that diagonals represent self-comparison weights, ensuring accurate self-similarity calculations. Additionally, the obikmer crate version has been bumped to 1.1.34.

src/Cargo.lock

@@ -1704,7 +1704,7 @@ dependencies = [
 
 [[package]]
 name = "obikmer"
-version = "1.1.33"
+version = "1.1.34"
 dependencies = [
  "clap",
  "csv",

src/obicompactvec/src/bitmatrix.rs

@@ -500,17 +500,26 @@ where T: Clone + Default {
 }
 
 /// Compute a symmetric `n×n` matrix in parallel by evaluating `f(i,j)` for
-/// all upper-triangle pairs. `T: Copy` avoids the `.clone()` needed for the
-/// lower-triangle mirror.
+/// all upper-triangle pairs, plus `f(i,i)` for the diagonal. `T: Copy` avoids
+/// the `.clone()` needed for the lower-triangle mirror.
+///
+/// The diagonal is *not* generally `T::default()`: for a self-comparison,
+/// `f(i,i)` is often the column's own weight (e.g. intersection-with-self —
+/// see `pairwise2_matrix`), not zero. Distance finalisations that need a
+/// zero diagonal (self-distance) already overwrite it explicitly.
 pub(crate) fn pairwise_matrix<T>(n: usize, f: impl Fn(usize, usize) -> T + Sync) -> Array2<T>
 where T: Copy + Default + Send {
     let results: Vec<(usize, usize, T)> = upper_pairs(n)
         .into_par_iter().map(|(i, j)| (i, j, f(i, j))).collect();
-    fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)))
+    let mut m = fill_symmetric(n, results.into_iter().map(|(i, j, v)| (i, j, v, v)));
+    for i in 0..n { m[[i, i]] = f(i, i); }
+    m
 }
 
 /// Same as `pairwise_matrix` but `f` returns two values that fill two
 /// symmetric matrices simultaneously (e.g. intersection + union for Jaccard).
+/// The diagonal is `f(i,i)` (e.g. a genome's kmer count intersected with
+/// itself), not `T::default()` — see `pairwise_matrix` for why that matters.
 pub(crate) fn pairwise2_matrix<T>(n: usize, f: impl Fn(usize, usize) -> (T, T) + Sync) -> (Array2<T>, Array2<T>)
 where T: Copy + Default + Send {
     let results: Vec<(usize, usize, T, T)> = upper_pairs(n)
@@ -523,5 +532,10 @@ where T: Copy + Default + Send {
         m0[[i, j]] = a; m0[[j, i]] = a;
         m1[[i, j]] = b; m1[[j, i]] = b;
     }
+    for i in 0..n {
+        let (a, b) = f(i, i);
+        m0[[i, i]] = a;
+        m1[[i, i]] = b;
+    }
     (m0, m1)
 }

src/obikmer/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "obikmer"
-version = "1.1.33"
+version = "1.1.34"
 edition = "2024"
 
 [[bin]]