Replace the quadratic paired-mapping search with linear-time sweep

src/chainer.rs

@@ -187,7 +187,7 @@ impl Chainer {
         let mut n_anchors = 0;
         let mut time_chaining = 0.0;
         let mut chains = vec![];
-        for is_revcomp in orientations {
+        for &is_revcomp in &orientations {
             let hits_timer = Instant::now();
             let mut anchors = hits_to_anchors(&hits[is_revcomp], index);
             time_find_hits += hits_timer.elapsed().as_secs_f64();
@@ -241,6 +241,7 @@ impl Chainer {
             time_chaining,
             time_rescue: 0.0,
             time_sort_nams: 0f64,
+            both_orientations: orientations.len() > 1,
         };
 
         (details, chains)

src/details.rs

@@ -23,6 +23,9 @@ pub struct NamDetails {
     pub time_chaining: f64,
     pub time_rescue: f64,
     pub time_sort_nams: f64,
+
+    /// Whether both orientations were tested
+    pub both_orientations: bool,
 }
 
 impl ops::AddAssign<NamDetails> for NamDetails {