Add benchmarks for the different `Threshold` implementations

lightmotif/benches/threshold.rs

+#![feature(test)]
+
+extern crate lightmotif;
+extern crate test;
+
+use lightmotif::abc::Dna;
+use lightmotif::num::StrictlyPositive;
+use lightmotif::num::U16;
+use lightmotif::num::U32;
+use lightmotif::pli::Pipeline;
+use lightmotif::pli::Score;
+use lightmotif::pli::StripedScores;
+use lightmotif::pli::Threshold;
+use lightmotif::pwm::CountMatrix;
+use lightmotif::seq::EncodedSequence;
+use lightmotif::seq::StripedSequence;
+
+const SEQUENCE: &str = include_str!("ecoli.txt");
+
+fn bench<C: StrictlyPositive, P: Score<Dna, C> + Threshold<C>>(
+    bencher: &mut test::Bencher,
+    pli: &P,
+) {
+    let mut striped = StripedSequence::<Dna, C>::encode(SEQUENCE).unwrap();
+
+    let cm = CountMatrix::<Dna>::from_sequences(&[
+        EncodedSequence::encode("GTTGACCTTATCAAC").unwrap(),
+        EncodedSequence::encode("GTTGATCCAGTCAAC").unwrap(),
+    ])
+    .unwrap();
+    let pbm = cm.to_freq(0.1);
+    let pssm = pbm.to_scoring(None);
+
+    striped.configure(&pssm);
+    let mut scores = StripedScores::empty();
+    pli.score_into(&striped, &pssm, &mut scores);
+
+    bencher.bytes = (std::mem::size_of::<f32>() * scores.len()) as u64;
+    bencher.iter(|| {
+        test::black_box(pli.threshold(&scores, 0.0));
+    });
+}
+
+#[bench]
+fn bench_generic(bencher: &mut test::Bencher) {
+    let pli = Pipeline::generic();
+    bench::<U32, _>(bencher, &pli);
+}
+
+#[cfg(target_feature = "sse2")]
+#[bench]
+fn bench_sse2(bencher: &mut test::Bencher) {
+    let pli = Pipeline::sse2().unwrap();
+    bench::<U16, _>(bencher, &pli);
+}
+
+#[cfg(target_feature = "sse2")]
+#[bench]
+fn bench_sse2_32(bencher: &mut test::Bencher) {
+    let pli = Pipeline::sse2().unwrap();
+    bench::<U32, _>(bencher, &pli);
+}
+
+#[cfg(target_feature = "avx2")]
+#[bench]
+fn bench_avx2(bencher: &mut test::Bencher) {
+    let pli = Pipeline::avx2().unwrap();
+    bench(bencher, &pli);
+}

lightmotif/src/pli/platform/sse2.rs

@@ -8,7 +8,6 @@ use std::ops::Div;
 use std::ops::Rem;
 
 use typenum::consts::U16;
-use typenum::consts::U4;
 use typenum::marker_traits::Unsigned;
 use typenum::marker_traits::Zero;
 
@@ -234,7 +233,7 @@ where
                     ((offset + 12) * data.rows()) as i32,
                 );
                 // Process rows iteratively
-                for (i, row) in data.iter().enumerate() {
+                for row in data.iter() {
                     // load scores for the current row
                     let r1 = _mm_load_ps(row[offset + 0x00..].as_ptr());
                     let r2 = _mm_load_ps(row[offset + 0x04..].as_ptr());

lightmotif/tests/dna.rs

@@ -95,6 +95,10 @@ fn test_threshold<C: StrictlyPositive, P: Score<Dna, C> + Threshold<C>>(pli: &P)
     let mut positions = pli.threshold(&result, -10.0);
     positions.sort_unstable();
     assert_eq!(positions, vec![18, 27, 32]);
+
+    let mut positions = pli.threshold(&result, -15.0);
+    positions.sort_unstable();
+    assert_eq!(positions, vec![10, 13, 14, 18, 24, 27, 32, 35, 40, 47]);
 }
 
 #[test]