Replace block-aligner with a custom SIMD aligner

Cargo.toml

@@ -21,12 +21,6 @@ flate2 = { version = "1.0", features = ["zlib-rs"]}
 thiserror = "2.0.11"
 rayon = "1.11.0"
 mimalloc = "0.1.48"
-[target.'cfg(target_arch = "wasm32-wasi")'.dependencies]
-block-aligner = { version = "0.5", features = ["simd_wasm"] }
-[target.'cfg(target_arch = "x86_64")'.dependencies]
-block-aligner = { version = "0.5", features = ["simd_avx2"] }
-[target.'cfg(target_arch = "aarch64")'.dependencies]
-block-aligner = { version = "0.5", features = ["simd_neon"] }
 
 [dev-dependencies]
 assert_cmd = "2.0.16"

src/aligner.rs

@@ -55,14 +55,14 @@ pub struct Aligner {
 }
 
 impl Aligner {
-    pub fn new(scores: Scores, k: usize, xdrop: i32) -> Self {
+    pub fn new(scores: Scores, k: usize, bandwidth: usize) -> Self {
         let ssw_aligner = SswAligner::new(
             scores.match_,
             scores.mismatch,
             scores.gap_open,
             scores.gap_extend,
         );
-        let piecewise_aligner = PiecewiseAligner::new(scores, k, xdrop);
+        let piecewise_aligner = PiecewiseAligner::new(scores, k, bandwidth);
         Aligner {
             scores,
             ssw_aligner,

src/cigar.rs

@@ -84,6 +84,12 @@ impl Cigar {
         Cigar { ops: vec![] }
     }
 
+    pub fn with_capacity(hint: usize) -> Self {
+        Cigar {
+            ops: Vec::with_capacity(hint),
+        }
+    }
+
     pub fn is_empty(&self) -> bool {
         self.ops.is_empty()
     }
@@ -124,6 +130,10 @@ impl Cigar {
         }
     }
 
+    pub fn reverse(&mut self) {
+        self.ops.reverse();
+    }
+
     pub fn extend(&mut self, other: &Cigar) {
         // TODO use push only for first, then extend
         for oplen in &other.ops {

src/lib.rs

@@ -20,4 +20,5 @@ pub mod refseq;
 pub mod revcomp;
 pub mod seeding;
 pub mod shuffle;
+pub mod simdaligner;
 pub mod ssw;

src/main.rs

@@ -267,9 +267,10 @@ struct Args {
     #[arg(long = "ssw", help_heading = "Alignment")]
     use_ssw: bool,
 
-    /// X-drop threshold for piecewise extension
-    #[arg(long = "xdrop", default_value_t = 500, value_name = "N", help_heading = "Alignment")]
-    xdrop: i32,
+    /// Bandwidth for the piecewise start/end extensions; extensions against a longer reference are
+    /// confined to this many diagonals off the anchor diagonal, shorter ones are aligned exactly
+    #[arg(long = "bw", default_value_t = 1024, value_name = "N", help_heading = "Alignment")]
+    bandwidth: usize,
 
 
     /// Path to input reference (in FASTA format)
@@ -537,7 +538,7 @@ fn run() -> Result<(), CliError> {
     debug!("{:?}", &scores);
 
     let chainer = Chainer::new(index.k(), chaining_parameters);
-    let aligner = Aligner::new(scores, index.k(), args.xdrop);
+    let aligner = Aligner::new(scores, index.k(), args.bandwidth);
 
     let cmd_line = env::args().skip(1).collect::<Vec<_>>().join(" ");
     let rg_id = match args.rg_id {