Minor cleanup

compare.sh

@@ -0,0 +1 @@
+RUSTFLAGS="-C target-cpu=native" cargo run --example compare --release -- "$@"

examples/compare.rs

@@ -91,10 +91,11 @@ fn main() {
     println!("Done!");
 }
 
+#[allow(dead_code)]
 #[allow(non_snake_case)]
 fn slow_align(q: &[u8], r: &[u8], x_drop: i32) -> i32 {
     let block_size = 32usize;
-    let step = 4usize;
+    let step = 8usize;
     //let step = 1usize;
 
     let mut D = vec![i32::MIN; (q.len() + 1 + block_size) * (r.len() + 1 + block_size)];
@@ -153,6 +154,7 @@ fn slow_align(q: &[u8], r: &[u8], x_drop: i32) -> i32 {
     }
 }
 
+#[allow(dead_code)]
 #[allow(non_snake_case)]
 fn block_max(D: &[i32], col_len: usize, start_i: usize, start_j: usize, block_width: usize, block_height: usize) -> i32 {
     let mut max = i32::MIN;
@@ -164,6 +166,7 @@ fn block_max(D: &[i32], col_len: usize, start_i: usize, start_j: usize, block_wi
     max
 }
 
+#[allow(dead_code)]
 #[allow(non_snake_case)]
 fn block_sum(D: &[i32], col_len: usize, start_i: usize, start_j: usize, block_width: usize, block_height: usize) -> i32 {
     let mut sum = 0;
@@ -175,6 +178,7 @@ fn block_sum(D: &[i32], col_len: usize, start_i: usize, start_j: usize, block_wi
     sum
 }
 
+#[allow(dead_code)]
 #[allow(non_snake_case)]
 fn calc_diag(q: &[u8], r: &[u8], D: &mut [i32], R: &mut [i32], C: &mut [i32], start_i: usize, start_j: usize, block_size: usize, gap_open: i32, gap_extend: i32) -> i32 {
     let idx = |i: usize, j: usize| { i + j * (q.len() + 1 + block_size) };
@@ -208,6 +212,7 @@ fn calc_diag(q: &[u8], r: &[u8], D: &mut [i32], R: &mut [i32], C: &mut [i32], st
     max
 }
 
+#[allow(dead_code)]
 #[allow(non_snake_case)]
 fn calc_block(q: &[u8], r: &[u8], D: &mut [i32], R: &mut [i32], C: &mut [i32], start_i: usize, start_j: usize, block_width: usize, block_height: usize, block_size: usize, gap_open: i32, gap_extend: i32) -> i32 {
     let idx = |i: usize, j: usize| { i + j * (q.len() + 1 + block_size) };

src/scan_block.rs

@@ -44,7 +44,7 @@ pub struct Block<'a, M: 'a + Matrix, const TRACE: bool, const X_DROP: bool> {
 }
 
 // increasing step size gives a bit extra speed but results in lower accuracy
-const STEP: usize = 4;
+const STEP: usize = 8;
 const LARGE_STEP: usize = 8; // use larger step size when the block size gets large
 const GROW_STEP: usize = L; // used when not growing by powers of 2
 const GROW_EXP: bool = true; // grow by powers of 2