Zoe v0.0.21

Release Notes for v0.0.21 - 2025-09-05

Added

• Added sw_simd_score_ends for getting the score and end coordinates of the alignment
• Added byte index map for amino acids, BLOSUM scoring matrices, and PAM scoring matrices
• Added display implementation for WeightMatrix
• Added get_subset to WeightMatrix for subsetting a weight matrix with a different alphabet
• Added parse_matrix for parsing a WeightMatrix from a file at compile time
• Added accessor byte_keys() for ByteIndexMap
• Added unchecked constructors for ScalarProfile and StripedProfile
• Added SamDataView and SamDataViewMut
• Added map attribute syntax to define_whichever and impl_traits, so that a map can be applied when implementing iterator
• Added dev-3pass feature gate for additional alignment functions that return coordinates, as well as a three-pass alignment function with reduced memory usage
• Added score_from_path and viterbi for LocalPhmm (behind dev-phmm feature gate)
• Added DomainPhmm, along with score_from_path for it (behind dev-phmm feature gate)
• Added SemiLocalPhmm, along with score_from_path and viterbi for it (behind dev-phmm feature gate)

Changed

• MaybeAligned now can hold other types besides Alignment, and score-only functions now return MaybeAligned<u32>
• into_biased_matrix has been renamed to to_biased_matrix and takes &self
• WeightMatrix is now imported under data::matrices in addition to data
• WeightMatrix now has an additional lifetime generic for the ByteIndexMap
• WeightMatrix no longer implements Copy
• The @ symbol is no longer included at the beginning of a header in a FastQ record (the reader strips it, and the display implementation re-adds it)
• Added tags field to SamData, as well as the ability to opt out of storing the tags in SamReader
• Changed Debug impl of CigarViewMut and derived more traits
• Various Smith-Waterman profile set methods have been moved to trait methods
  for ProfileSets.
• Updated traceback in viterbi to not use nested vecs (behind dev-phmm feature gate)
• Removed as_u32 from Alignment, since the integer type for scores has been standardized

Fixes

• Fixes a bug in AlignmentStates::add_ciglet() for inc > 1