Skip first l-1 kmer-ambiguity iterations

Author: RagnarGrootKoerkamp

src/lib.rs

@@ -426,7 +426,7 @@ impl<'s, 'o, const CANONICAL: bool, SEQ: Seq<'s>> Output<'o, CANONICAL, SEQ> {
     /// Iterator over positions and (canonical) u64 kmer-values associated with all minimizer positions.
     #[must_use]
     pub fn pos_and_values_u64(&self) -> impl ExactSizeIterator<Item = (u32, u64)> {
-        self.min_pos.iter().map(move |&pos| {
+        self.min_pos.iter().map(#[inline(always)] move |&pos| {
             let val = if CANONICAL {
                 let a = self.seq.read_kmer(self.k, pos as usize);
                 let b = self.seq.read_revcomp_kmer(self.k, pos as usize);
@@ -440,7 +440,7 @@ impl<'s, 'o, const CANONICAL: bool, SEQ: Seq<'s>> Output<'o, CANONICAL, SEQ> {
     /// Iterator over positions and (canonical) u128 kmer-values associated with all minimizer positions.
     #[must_use]
     pub fn pos_and_values_u128(&self) -> impl ExactSizeIterator<Item = (u32, u128)> {
-        self.min_pos.iter().map(move |&pos| {
+        self.min_pos.iter().map(#[inline(always)] move |&pos| {
             let val = if CANONICAL {
                 let a = self.seq.read_kmer_u128(self.k, pos as usize);
                 let b = self.seq.read_revcomp_kmer_u128(self.k, pos as usize);

src/minimizers.rs

@@ -183,25 +183,27 @@ pub fn canonical_minimizers_skip_ambiguous_windows<'s>(
     let (c_delay, mut canonical_mapper) = canonical_mapper_simd(l);
 
     let mut padded_it = seq
-        .par_iter_bp_delayed_2_with_factor(l, hasher.delay(), c_delay, 2)
-        .zip(bitseq.par_iter_kmer_ambiguity(l, l));
+        .par_iter_bp_delayed_2_with_factor(l, hasher.delay(), c_delay, 2);
 
     // Process first k-1 characters separately, to initialize hash values.
-    padded_it.advance_with(k - 1, |((a, rh, rc), _ambi)| {
+    padded_it.advance_with(k - 1, |(a, rh, rc)| {
         hash_mapper((a, rh));
         canonical_mapper((a, rc));
     });
     let mut sliding_min_mapper = sliding_lr_min_mapper_simd(w, padded_it.it.len(), cache);
-    padded_it.advance_with(w - 1, |((a, rh, rc), _ambi)| {
+    padded_it.advance_with(w - 1, |(a, rh, rc)| {
         let hash = hash_mapper((a, rh));
         canonical_mapper((a, rc));
         sliding_min_mapper(hash);
     });
 
-    padded_it.map(move |((a, rh, rc), ambi)| {
+    // jump over the l-1 first ambiguity results
+    padded_it
+        .zip(bitseq.par_iter_kmer_ambiguity(l, l, l-1))
+        .map(move |((a, rh, rc), ambi)| {
         let hash = hash_mapper((a, rh));
         let canonical = canonical_mapper((a, rc));
         let (lmin, rmin) = sliding_min_mapper(hash);
-        ambi.blend(u32x8::splat(u32::MAX - 1), canonical.blend(lmin, rmin))
+        ambi.blend(u32x8::splat(SKIPPED), canonical.blend(lmin, rmin))
     })
 }