Add iter_{canonical}_minimizer_values_u128

Author: RagnarGrootKoerkamp

CHANGELOG.md

@@ -1,7 +1,11 @@
 # Changelog
 
+## 1.3
+- Update to `packed-seq` `3.2.1` for `u128` kmer value support.
+- Add `iter_{canonical}_minimizer_values_u128` to iterate over `u128` kmer values.
+
 ## 1.2
-- Fix #10: Add `extract_{canonical}_minimizer_values` to convert positions into `u64` kmer values.
+- Fix #10: Add `iter_{canonical}_minimizer_values` to convert positions into `u64` kmer values.
 - Update to `packed-seq` `3.0`.
 - Fix to properly initialize arrays when collecting super-k-mers.
 - Update `packed-seq` to support non-byte offsets.

simd-minimizers/src/lib.rs

@@ -304,6 +304,36 @@ pub fn iter_canonical_minimizer_values<'s, S: Seq<'s>>(
     })
 }
 
+/// Given a sequence and a list of positions, iterate over the k-mer values at those positions.
+#[inline(always)]
+pub fn iter_minimizer_values_u128<'s, S: Seq<'s>>(
+    seq: S,
+    k: usize,
+    positions: &'s [u32],
+) -> impl ExactSizeIterator<Item = u128> + Captures<&'s ()> + Clone {
+    positions
+        .iter()
+        .map(move |&pos| seq.read_kmer_u128(k, pos as usize))
+}
+
+/// Given a sequence and a list of positions, iterate over the *canonical* k-mer values at those positions.
+///
+/// Canonical k-mers are defined as the *minimum* of the k-mer and its reverse complement.
+/// Note that this also works for even `k`, but typically one would want `k` to be odd.
+#[inline(always)]
+pub fn iter_canonical_minimizer_values_u128<'s, S: Seq<'s>>(
+    seq: S,
+    k: usize,
+    positions: &'s [u32],
+) -> impl ExactSizeIterator<Item = u128> + Captures<&'s ()> + Clone {
+    positions.iter().map(move |&pos| {
+        let a = seq.read_kmer_u128(k, pos as usize);
+        let b = seq.read_revcomp_kmer_u128(k, pos as usize);
+        core::cmp::min(a, b)
+    })
+}
+
+
 /// Variants that always use mulHash, instead of the default ntHash for DNA and mulHash for text.
 pub mod mul_hash {
     use super::*;