Release v0.0.28

Author: willchet

CHANGELOG.md

@@ -4,27 +4,30 @@ All notable changes to this project will be documented in this file. The format
 is roughly based on [Keep a Changelog], and this project tries to adheres to
 [Semantic Versioning].
 
-## [0.0.28] - TBD
+## [0.0.28] - 2026-04-29
 
 ### Added
 
-- `Nucleotides` and `AminoAcids` (and view types) can now be converted into `Vec`, slices, and `Cow` using `From` 
-- `NucleotidesView`, `AminoAcidsView`, and `QualityScoresView` now have inherent `slice` methods offering a longer lifetime of the returned view
-- Added `as_map` accessor to convert `ByteIndexMap` to `ByteMap`
 - Similar to the `OrFail` trait for `Result`, a `Fail` trait has been introduced to handle errors directly
 - Added `*_mapped` versions for many string/byte search functions, which search a lazily-mapped haystack
+- Added `as_map` accessor to convert `ByteIndexMap` to `ByteMap`
+- `Nucleotides` and `AminoAcids` (and view types) can now be converted into `Vec`, slices, and `Cow` using `From` 
+- `NucleotidesView`, `AminoAcidsView`, and `QualityScoresView` now have inherent `slice` methods offering a longer lifetime of the returned view
 
 ### Changed
 
 - `LocalProfiles` and `SharedProfiles` now can hold either a borrowed or an owned sequence, enabling sequences and profiles to be stored in the same struct without becoming self-referential
 - `CigletIterator` now yields empty ciglets when a CIGAR string contains an explicit increment that is 0. A missing increment field ends the iterator early
-- `find_mapped_match_simd` now only supports lane counts greater than 2
+- `find_mapped_match_simd` better handles needles with a single repeating byte, but now only supports lane counts greater than 2
 
 ### Fixed
 
-- Subsequent calls to `next_back` in `CigletIterator` now properly return `None` after invalid state is reached
+- Fixed incorrect ranges returned by `Alignment::to_reverse` and `Alignment::make_reverse`
 - Methods in `StatesSequence` and `StatesSequenceMut` now properly skip empty `Ciglet`s (with an increment of 0)
 - Pre-alignment filter `sneaky_snake` now properly handles inputs with length differences greater than provided threshold.
+- Subsequent calls to `next_back` in `CigletIterator` now properly return `None` after invalid state is reached
+- Equality comparisons between `Cigar` and `AlignmentStates` now properly return false for an overflowing increment
+- Fixes the potential of overflow in `hamming`
 
 ## [0.0.27] - 2026-04-15
 

Cargo.lock

@@ -1,7 +1,7 @@
 [package]
 edition = "2024"
 name = "zoe"
-version = "0.0.28-dev"
+version = "0.0.28"
 rust-version = "1.95"
 description = "A nightly library for viral genomics"
 license = "Apache-2.0"

Cargo.toml

@@ -49,9 +49,9 @@ pub(crate) fn validate_profile_args(seq: &[u8], gap_open: i8, gap_extend: i8) ->
 /// in an alignment. The API mirrors that of [`StripedProfile`], but this
 /// profile does not use SIMD or create a striped layout.
 ///
-/// ## Type Parameters
+/// ## Parameters
 ///
-/// `S` - The size of the alphabet (usually 5 for DNA including *N*)
+/// `S`: The size of the alphabet (usually 5 for DNA including *N*)
 #[derive(Clone, Eq, PartialEq, Debug)]
 pub struct ScalarProfile<'a, const S: usize> {
     pub(crate) seq:        Cow<'a, [u8]>,
@@ -186,13 +186,14 @@ impl<'a, const S: usize> ScalarProfile<'a, S> {
 /// specified mapping, arranged in a striped pattern to optimize SIMD operations
 /// during alignment.
 ///
-/// ## Type Parameters
+/// ## Parameters
 ///
-/// - `T` - The numeric type used for scores. `i8`, `i16`, `i32`, and `i64` use
+/// - `'a`: The lifetime of the alphabet ([`ByteIndexMap`]).
+/// - `T`: The numeric type used for scores. `i8`, `i16`, `i32`, and `i64` use
 ///   the signed algorithm, which is the most common. `u8`, `u16`, `u32`, and
 ///   `u64` use the unsigned algorithm.
-/// - `N` - The number of SIMD lanes (usually 16, 32 or 64).
-/// - `S` - The size of the alphabet (usually 5 for DNA including `N`).
+/// - `N`: The number of SIMD lanes (usually 16, 32 or 64).
+/// - `S`: The size of the alphabet (usually 5 for DNA including `N`).
 #[derive(Debug, Clone, PartialEq, Eq, Hash)]
 pub struct StripedProfile<'a, T, const N: usize, const S: usize>
 where

src/alignment/profile.rs

@@ -10,12 +10,12 @@ use std::{borrow::Cow, cell::OnceCell, sync::OnceLock};
 /// convenience methods for automatically increasing the integer width and
 /// rerunning the alignment when overflow occurs.
 ///
-/// ## Type Parameters
+/// ## Parameters
 ///
-/// - `M` - The number of SIMD lanes for `i8` profiles.
-/// - `N` - The number of SIMD lanes for `i16` profiles.
-/// - `O` - The number of SIMD lanes for `i32` profiles.
-/// - `S` - The size of the alphabet (usually 5 for DNA including `N`).
+/// - `M`: The number of SIMD lanes for `i8` profiles.
+/// - `N`: The number of SIMD lanes for `i16` profiles.
+/// - `O`: The number of SIMD lanes for `i32` profiles.
+/// - `S`: The size of the alphabet (usually 5 for DNA including `N`).
 pub trait ProfileSets<'a, const M: usize, const N: usize, const O: usize, const S: usize>: Sized {
     /// Gets or initializes [`StripedProfile`] with elements of `i8` and `M`
     /// SIMD lanes and returns a reference to the field.
@@ -368,12 +368,16 @@ pub trait ProfileSets<'a, const M: usize, const N: usize, const O: usize, const
 /// If it is necessary to share between multiple threads, consider using
 /// [`SharedProfiles`].
 ///
-/// ## Type Parameters
+/// ## Parameters
 ///
-/// - `M` - The number of SIMD lanes for `i8` profiles.
-/// - `N` - The number of SIMD lanes for `i16` profiles.
-/// - `O` - The number of SIMD lanes for `i32` profiles.
-/// - `S` - The size of the alphabet (usually 5 for DNA including `N`).
+/// - `'a`: The lifetime of the stored sequence, the [`WeightMatrix`], and the
+///   alphabet ([`ByteIndexMap`]). An owned sequence can also be stored.
+/// - `M`: The number of SIMD lanes for `i8` profiles.
+/// - `N`: The number of SIMD lanes for `i16` profiles.
+/// - `O`: The number of SIMD lanes for `i32` profiles.
+/// - `S`: The size of the alphabet (usually 5 for DNA including `N`).
+///
+/// [`ByteIndexMap`]: crate::data::ByteIndexMap
 #[derive(Debug, Clone)]
 pub struct LocalProfiles<'a, const M: usize, const N: usize, const O: usize, const S: usize> {
     pub(crate) seq:         Cow<'a, [u8]>,
@@ -534,12 +538,16 @@ impl<'a, const M: usize, const N: usize, const O: usize, const S: usize> Profile
 /// When sharing between threads is not needed, consider using [`LocalProfiles`]
 /// instead.
 ///
-/// ## Type Parameters
+/// ## Parameters
+///
+/// - `'a`: The lifetime of the stored sequence, the [`WeightMatrix`], and the
+///   alphabet ([`ByteIndexMap`]). An owned sequence can also be stored.
+/// - `M`: The number of SIMD lanes for `i8` profiles
+/// - `N`: The number of SIMD lanes for `i16` profiles
+/// - `O`: The number of SIMD lanes for `i32` profiles
+/// - `S`: The size of the alphabet (usually 5 for DNA including *N*)
 ///
-/// - `M` - The number of SIMD lanes for `i8` profiles
-/// - `N` - The number of SIMD lanes for `i16` profiles
-/// - `O` - The number of SIMD lanes for `i32` profiles
-/// - `S` - The size of the alphabet (usually 5 for DNA including *N*)
+/// [`ByteIndexMap`]: crate::data::ByteIndexMap
 #[derive(Debug, Clone)]
 pub struct SharedProfiles<'a, const M: usize, const N: usize, const O: usize, const S: usize> {
     pub(crate) seq:         Cow<'a, [u8]>,

src/alignment/profile_set.rs

@@ -637,10 +637,10 @@ where
 ///
 /// ## Parameters
 ///
-/// - `T` - The integer type whose max score is being computed.
-/// - `U` - The integer type used in the [`WeightMatrix`], which must be of the
+/// - `T`: The integer type whose max score is being computed.
+/// - `U`: The integer type used in the [`WeightMatrix`], which must be of the
 ///   same sign as `T`.
-/// - `S` - The alphabet size.
+/// - `S`: The alphabet size.
 ///
 /// <div class="warning note">
 ///

src/alignment/sw/striped.rs

@@ -212,7 +212,7 @@ impl ByteMap {
 /// For example, this could be a map from DNA bases to profile indices, such as
 /// [`DNA_PROFILE_MAP`].
 ///
-/// ## Type Parameters
+/// ## Parameters
 ///
 /// `S`: The number of unique indices in the output of the mapping (such as 5
 /// for DNA including *N*)

src/data/constants/mappings/byte_index.rs

@@ -26,9 +26,9 @@ pub(crate) use tabulation::{hamming_dist_from_sub_matrix, total_and_frequencies}
 ///
 /// `None` is returned if no valid positions are found to compare.
 ///
-/// ## Type Parameters
+/// ## Parameters
 ///
-/// `N` - SIMD lane count, must be a supported lane count
+/// `N`: SIMD lane count, must be a supported lane count
 ///
 /// ## Example
 ///

src/distance/dna/mod.rs

@@ -84,7 +84,7 @@ impl<'a, const N: usize> Iterator for SplitByByte2<'a, N> {
 ///
 /// ## Parameters
 ///
-/// `N` - The number of SIMD lanes to use.
+/// `N`: The number of SIMD lanes to use.
 #[inline]
 #[must_use]
 #[cfg_attr(feature = "multiversion", multiversion::multiversion(targets = "simd"))]
@@ -99,7 +99,9 @@ pub fn position_by_byte<const N: usize>(haystack: &[u8], b: u8) -> Option<usize>
 ///
 /// ## Parameters
 ///
-/// `N` - The number of SIMD lanes to use.
+/// - `N`: The number of SIMD lanes to use.
+/// - `S`: The SIMD-vectorized mapping to lazily apply to the `haystack`.
+/// - `B`: The non-vectorized mapping to lazily apply to the `haystack`.
 #[inline]
 #[must_use]
 #[cfg_attr(feature = "multiversion", multiversion::multiversion(targets = "simd"))]
@@ -151,7 +153,7 @@ where
 ///
 /// ## Parameters
 ///
-/// `N` - The number of SIMD lanes to use.
+/// `N`: The number of SIMD lanes to use.
 #[inline]
 #[must_use]
 #[cfg_attr(feature = "multiversion", multiversion::multiversion(targets = "simd"))]
@@ -166,7 +168,9 @@ pub fn position_by_byte2<const N: usize>(haystack: &[u8], b1: u8, b2: u8) -> Opt
 ///
 /// ## Parameters
 ///
-/// `N` - The number of SIMD lanes to use.
+/// - `N`: The number of SIMD lanes to use.
+/// - `S`: The SIMD-vectorized mapping to lazily apply to the `haystack`.
+/// - `B`: The non-vectorized mapping to lazily apply to the `haystack`.
 #[inline]
 #[must_use]
 #[cfg_attr(feature = "multiversion", multiversion::multiversion(targets = "simd"))]
@@ -221,7 +225,7 @@ where
 ///
 /// ## Parameters
 ///
-/// `N` - The number of SIMD lanes to use.
+/// `N`: The number of SIMD lanes to use.
 #[inline]
 #[must_use]
 #[cfg_attr(feature = "multiversion", multiversion::multiversion(targets = "simd"))]
@@ -253,8 +257,9 @@ pub fn position_by_byte3<const N: usize>(haystack: &[u8], b1: u8, b2: u8, b3: u8
 ///
 /// The following parameters can be used to adjust performance characteristics:
 ///
-/// - `N` - The number of SIMD lanes to use.
-/// - `UF` - The unroll factor, which must be non-zero.
+/// - `N`: The number of SIMD lanes to use.
+/// - `UF`: The unroll factor, which must be non-zero.
+/// - `P`: The SIMD-vectorized predicate for identifying matching bytes.
 #[inline]
 #[must_use]
 #[allow(clippy::needless_range_loop)]

src/search/bytes/search.rs

@@ -71,8 +71,8 @@ const fn create_masks<const N: usize>() -> [Simd<u8, N>; 256] {
 ///
 /// ## Parameters
 ///
-/// - `N` - The number of SIMD lanes to use.
-/// - `K` - The number of differences allowed.
+/// - `N`: The number of SIMD lanes to use.
+/// - `K`: The number of differences allowed.
 ///
 /// ## Limitations
 ///