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Changelog

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0.2.6

  • Support max_n_frac directly in the Searcher API, rather than only in the CLI. A small breaking change removes the max_n_frac argument from Searcher::search_all_alignents. (#66, #67)

0.2.5

  • Fix that Searcher::without_trace was ignored. Specifically this made search_all and search_all_alignments unnecessarily slow. (#65)

0.2.4

  • Add Searcher::search_all_alignments that returns a list of all possible alignments of cost up to k for each matching end position. of cost up to k (#46, #55, #56, #57, #63). Thanks to @theJasonFan and @TimD1!
  • Bump cargo-multivers to 0.12.0 to fix running x86 emulation on macbooks (#64).
  • Fix name of binary in cargo help (#64).
  • Improved layout of statistics on number of matches.
  • Improved rendering in ASCII mode.

0.2.3

  • Add grep-like sassy agrep for searching plain-text files.
  • search_many and search_texts now accept any slice where the elements implement RcSearchable, not just a slice of references to a type implementing RcSearchable. This means that in some cases there is no need to create a temporary Vec just to hold texts references (#60).
  • Fix SearchMode not being public, making search_many useless outside the Python bindings.

0.2.2

  • Build GitHub x86-64 binaries for both AVX2 and AVX-512 using cargo multivers.

0.2.1

  • Breaking: Tracebacks now prefer substitutions over indels, as this is more practically useful: #46 (Previous behaviour was to prefer matches, and otherwise deletion over substitution over insertion.)
  • docs: Add Rust and CLI examples for v2 to the readme
  • docs: Clarify the tsv output of sassy search in the readme.
  • docs: Clarify overhang #37
  • feat: Add sassy grep --v2 for searching based on the algorithm of the v2 paper.
  • feat: Add sassy search --sam flag to report negative-strand matches and CIGARs in the text direction, rather than the default of reverse-complementing them to match the pattern direction. #49
  • feat: Add sassy crispr --pam-length <len> to allow changing the default of 3.
  • python: Add python typing #43
  • misc: Introduce default-enabled cli and diagnostics features to allow pruning dependencies and building for WASM. #50 #51 redundant dependencies.
  • misc: Refactors to share traceback code between v1 and v2.
  • evals: Updates to v1 and v2 evals.

0.2.0

The main new feature of this v2 release is search_encoded_patterns, written by @RickBeeloo, for searching many short and equal length patterns (say 23 bp; should be at most 32 or else 64) in parallel. This is 2x or more faster than eg search_patterns, because it packs deltas in the pattern (rather than text) direction, which removes a lot of overhead in the 'early break check' and makes the 'profile' much faster.

v2 also adds new variants of the existing Searcher::search method:

  • search_patterns: search multiple similar-length patterns in a single text. Useful for searching in short texts where chunking them in pieces via the normal search has large overhead. This uses one SIMD lane per pattern.
  • search_texts: search a single pattern in multiple similar-length texts. This uses one SIMD lane per text.
  • search_many: a more high-level wrapper that takes a list of patterns and texts and does an all-vs-all search on multiple threads, using a user-specified underlying algorithm.

Further changes:

  • Breaking: Cigar output now follows the SAM spec and reversed I and D compared to before. I now means the pattern contains a character that is not in the text.
  • feat: Support AVX512 for pattern tiling.
  • feat: moved pretty printing from bin/grep.rs to publicly available Match::pretty_print.
  • feat: Match now contains text_idx and pattern_idx for multi-search variants.
  • feat: Add Searcher::only_best_match and Searcher::without_trace.
  • perf: Collect matches into an internal Vec before returning that.
  • fix: sassy grep would crash on printing reverse complement matches with overhang.
  • fix: fix issues with duplicate reported matches in overhang
  • misc: debug-printing a Match now uses stringified cigar.
  • misc: Add python bindings for search_many

0.1.10

  • bugfix: sassy grep had a bug in the batching logic, making it skip a record after every 1MB of input. So for human genomes it would only search every other record.
  • docs: Recommend to use Profile::Iupac instead of Profile::Dna in docs and examples. (#38)
  • misc: set up cargo release

0.1.9

  • Implement RcSearchable for ?Sized types such as [u8], so that seach(_, text, _) now works for text: &[u8], instead of only text: &&[u8].
  • Migrate back from cargo-dist to a small manual release.yaml.
  • Abort on panic.

0.1.8

  • Sassy is now available on bioconda!
  • ci: add aarch64-linux target for github releases, drop windows targets
  • ci: by default target-cpu=native, but config-portable.yaml for CI builds
  • doc: readme updates for target-cpu
  • update to ensure_simd for compile-time AVX2 check and add a run-time check as well.

0.1.7

  • Improved compile error message when not using -target-cpu=native. (#37)
  • Added installation section to README, explaining the use of RUSTFLAGS and minimal required rust version. (#37)
  • Assert whether the selected profile supports overhang.
  • Add cargo-dist for binary release artefacts.
  • Move some internal features from feature-gated to #[doc(hidden)] mod private {}.

0.1.6

  • feat: Use wide instead of portable-simd so that sassy now works on stable Rust (#26). It's slightly (<5%) slower and has slightly ugly code, but good enough for now.

0.1.5

  • feat: Add sassy search, sassy filter, and sassy grep (#35, see updated readme).
  • perf: Improvements when searching short (len ~16) patterns, by avoiding redundant expensive find_mininima call.
  • perf: Improvements when searching short texts without overhang, by avoiding redundant floating point operations.
  • misc: Bump pa-types to 1.2.0 for Cigar::to_char_pairs to conveniently iterate over corresponding characters.
  • misc: derive(Clone) for Searcher (#36)
  • misc: Bugfix for mixed-case IUPAC input.
  • docs: Minor documentation & readme fixes.

0.1.4

  • Improve docs for sassy crispr (#34 by @tfenne).
  • Require value for --max-n-frac (#33 by @tfenne).
  • Check that AVX2 or NEON instructions are enabled; otherwise -F scalar is required.
  • Non-x86 support: Use swizzle_dyn instead of hardcoding _mm256_shuffle_epi8.
  • Add fallback for non-BMI2 instruction sets; 5-20% slower.
  • Update pa-types to 1.1.0 for CIGAR output that always includes 1 (eg 1=).
  • Fix/invert sassy crispr --no-rc flag.
  • Ensure output columns of sassy crispr match content (#31 by @tfenne).

0.1.3

  • Include source code in pypi distribution.

0.1.2

  • First public release on crates.io and pypi.