Add pack_kmer_lossy function that converts a slice of ASCII into its u64 representation

Author: RagnarGrootKoerkamp

src/lib.rs

@@ -142,9 +142,9 @@ pub use ascii_seq::{AsciiSeq, AsciiSeqVec};
 pub use packed_n_seq::{PackedNSeq, PackedNSeqVec};
 pub use packed_seq::{BitSeq, BitSeqVec, PackedSeq, PackedSeqVec};
 pub use packed_seq::{
-    complement_base, complement_base_simd, complement_char, pack_char, unpack_base, unpack_kmer,
-    unpack_kmer_into_vec, unpack_kmer_to_vec, unpack_kmer_u128, unpack_kmer_u128_into_vec,
-    unpack_kmer_u128_to_vec,
+    complement_base, complement_base_simd, complement_char, pack_char, pack_kmer_lossy,
+    pack_kmer_u128_lossy, unpack_base, unpack_kmer, unpack_kmer_into_vec, unpack_kmer_to_vec,
+    unpack_kmer_u128, unpack_kmer_u128_into_vec, unpack_kmer_u128_to_vec,
 };
 pub use padded_it::{Advance, ChunkIt, PaddedIt};
 pub use traits::{Delay, Seq, SeqVec};

src/packed_seq.rs

@@ -216,6 +216,25 @@ pub fn pack_char(base: u8) -> u8 {
 pub fn pack_char_lossy(base: u8) -> u8 {
     (base >> 1) & 3
 }
+/// Pack a slice of ASCII `ACTGactg` characters into its packed 2-bit kmer representation.
+/// Other characters are silently converted.
+#[inline(always)]
+pub fn pack_kmer_lossy(slice: &[u8]) -> u64 {
+    let mut kmer = 0;
+    for (i, &base) in slice.iter().enumerate() {
+        kmer |= (pack_char_lossy(base) as u64) << (2 * i);
+    }
+    kmer
+}
+/// Pack a slice of ASCII `ACTGactg` characters into its packed 2-bit kmer representation.
+#[inline(always)]
+pub fn pack_kmer_u128_lossy(slice: &[u8]) -> u128 {
+    let mut kmer = 0;
+    for (i, &base) in slice.iter().enumerate() {
+        kmer |= (pack_char_lossy(base) as u128) << (2 * i);
+    }
+    kmer
+}
 
 /// Unpack a 2-bit DNA base into the corresponding `ACTG` character.
 #[inline(always)]