v0.2.3

• Add sassy agrep for a simple grep-like CLI over ASCII files.
• Small improvements.

v0.2.2: AVX-512 enabled binary

This release is identical to before, but uses cargo multivers to build a binary for x86-64 that transparently works on both AVX2 and AVX-512.

v0.2.1: tracebacks prefer substitutions & more

New release with a bunch of small improvements. See the changelog for details.

Important: tracebacks now prefer substitutions over deletions, whereas before they preferred deletions.

Otherwise:

• improved docs and examples
• additional optional feature flags that can be disabled to speed up compilation
• sassy search --sam flag to follow the SAM spec when outputting reverse-complement matches. By default we reverse-complement the text and CIGAR to align with the pattern direction, but with this flag we do not.

v0.2.0

New v2 search functions

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 the previous search_patterns.

(Improved docs and examples for these new features are still TODO. This release was mostly triggered by breaking changes to the cigar output.)

Breaking changes

• Cigar output now follows the SAM spec and reverses I and D
  compared to before. I now means the pattern contains a character that is not
  in the text.

Further new search functions

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

• 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

v0.1.10: critical bugfix in `sassy grep` CLI

• critical bugfix: sassy grep had a bug in the batching logic, making it skip a
  record after every 1MB of input. In particular for human genomes it would only search
  every other chromosome...
• misc: set up cargo release

v0.1.9

Release 0.1.9

Changelog for 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].
• Abort on panic for slightly smaller binaries.
• Migrate back from cargo-dist to a small manual release.yaml.

Changelog for 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

Release Notes

• 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 artifacts.

Download sassy 0.1.7

File	Platform	Checksum
sassy-aarch64-apple-darwin.tar.xz	Apple Silicon macOS
sassy-x86_64-unknown-linux-gnu.tar.xz	x64 Linux