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Changelog

git

4.4.2

  • Bugfix on 32-bit platforms where reverse-complementing k-mers used usize::BITS instead of u64::BITS.

4.4.1

  • Improve docs

4.4.0

  • Add PackedSeq{Vec}Base::from_raw_parts to construct directly from a Vec or slice.
  • Add PackedNSeqVec::from_ascii_and_quality that masks out low-quality bases.
  • Add PackedNSeqVec::from_{fastx,fastq_with_quality} behind file_io feature (for needletail dependency).
  • Add experimental PackedEfNSeq that stores N positions in an EF vector, behind ef_seq feature flag (for sux dependency).

4.3.0

  • Add unpack_kmer_to_vec(kmer: u64, k) -> Vec and variants.
  • Add pack_kmer_lossy(kmer: &[u8]) -> u64 and variants.
  • switch to ensure_simd

4.2.0

  • Perf: improve NEON codegen by avoiding u32x8::splat.
  • Perf: reuse thread-local allocations between invocations
  • Feat: par_iter_bp_*_with_buf versions that allow passing in buffers from the stack, which can be slightly faster than thread-locals.
  • Perf: all PackedSeq slices have padding to allow faster out-of-bounds reading.
  • Perf: Rewrite par_iter_kmer_ambiguity to use a delayed iterator.
  • Feat: Add PackedNSeq::slice(Range<usize>) utility.

4.1.1

  • Feat: PackedNSeqVec::{default,clear,push_ascii}.
  • Feat: BitSeqVec::par_iter_kmer_ambiguity supports k up to 96.

4.1.0

  • Perf: Further optimizations to BitSeq::from_ascii and PackedSeq::from_ascii for both AVX and NEON. (Fewer out-of-bounds checks, NEON optimizations to work around lack of movemask.)
  • Perf: Add small benchmarks (in src/test.rs) for {Bit,Packed}Seq::push_ascii and PackedSeq::par_iter_bp.
  • Perf: More #[inline(always)] for better performance with lto="thin".
  • Feature: Add BitSeqVec::random.
  • Feature: Add PackedNSeq as a wrapper around (PackedSeq, BitSeq) to hold 2+1-bit encoded data, with the first 2 bits encoding ACGT, and the last bit indicating non-ACGT IUPAC characters (such as N, R, Y, ...).
  • Feature: Add PackedSeq::par_iter_bp_delayed_with_factor (mirring par_iter_bp_delayed_2_with_factor) for use in seq-hash.
  • Bugfix for repeated BitSeq::push_ascii.
  • Bugfix for BitSeq::to_revcomp (which was still 'complementing' instead of only reversing).

4.0.1

  • Feature: optimize BitSeq::from_ascii for NEON.
  • Bugfix: 1-bit reverse was also doing 'complement'.

4.0.0

  • Feature: Add BitSeq and BitSeqVec as 1-bit encoded 'sequences' that by default indicate the positions of ambiguous (non-ACTG) characters.
  • Feature: Add BitSeq::par_iter_kmer_ambiguity that returns for each kmer whether it contains an ambiguous base.
  • Breaking: Encapsulate parallel iterators in new PaddedIt { it, padding: usize } type with .map, .advance, zip, and .collect_into functions.
  • Breaking: Make delay passed into par_iter_bp_delayed a strong type Delay(pub usize) to reduce potential for bugs.
  • Make intrinsics::transpose public for use in collect_and_dedup in simd_minimizers.

3.2.1

  • Add Seq::read_{revcomp}_kmer_u128 with more tests
  • Fix bug in revcomp_u128

3.2.0: yanked

  • Add Seq::as_u128 and Seq::revcomp_as_u128
  • revcomp_u128 had a bug; fixed in 3.2.1

3.1

  • PackedSeqVec::{from,push}_ascii now silently convert non-ACGT characters to values in 0..4, instead of inconsistently only panicking for non-ACGT near the sequence start and end.

3.0

  • Speed up PackedSeqVec::push_ascii() on ARM
  • Add Seq::to_revcomp().
  • Add PackedSeqVec::clear().
  • PackedSeq::as_u64 now supports k up to 32, instead of only up to 29. (Fixes #2.)
  • PackedSeqVec::get now uses checked indexing, to prevent unsafe out-of-bounds access.
  • Breaking: PackedSeqVec and PackedSeq fields are now private, to uphold internal padding guarantees.
  • Add convenience methods {Seq, SeqVec}::{read_kmer, read_revcomp_kmer} as shorthands for .slice(pos..pos+k).as_u64().
  • Deprecate to_word and to_word_revcomp. Instead as_u64 and revcomp_as_u64 are added. ('word' is not very clear, and u64 makes more sense for kmers than usize.)
  • Support par_iter_bp for sequences that do not start at byte offsets.
  • Add packed_seq::revcomp_u64() and Seq::revcomp_as_u64() for reverse complementing kmers.
  • Make random dependency optional but enabled by default (so it can be disabled for wasm backends).

2.0

  • Change from tuples of (simd iterator, scalar tail iterator) to returning only a simd iterator and padding: usize that indicates the number of padded elements at the back that should be ignored.

1.0

  • Initial release.