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Changelog

Unreleased

Added

  • --max-decompression-size CLI option to set a safety limit against decompression bombs (default 4 GiB, 0 = unlimited)
  • Structured error handling with actionable messages for common issues (unwritable output, missing directories, decompression limits, CSV format errors)
  • 260 tests: unit, integration, property-based (proptest), snapshot (insta), fuzz regression, and validation
  • Criterion benchmarks for matching, parsing, pipeline, and circular genome operations
  • Complete public API documentation enforced by missing_docs lint
  • CI quality gate on every push and pull request (rustfmt, clippy pedantic, cargo-deny, coverage with Codecov)

Changed

  • Internal: extracted pipeline logic to src/pipeline.rs, unified GenBank parser, adaptive buffer sizing

v0.2.0

Current release.

  • SIMD-accelerated approximate primer matching via sassy
  • Full IUPAC ambiguity code support in primers
  • FASTA and GenBank input with automatic format detection
  • Circular genome support with wrap-around product detection
  • Reverse complement strand search
  • Multi-threaded file reading, searching, and compression
  • Gzip/BGZF transparent compression for input and output
  • Flexible primer input via command line or CSV file
  • TSV statistics output with alignment details (CIGAR strings, identity scores)
  • Configurable product length filtering and N-base fraction limits
  • Duplicate product removal (canonicalized by reverse complement)
  • Progress bar with run summary
  • Two FASTA parser backends: seq_io (default) and needletail
  • Available via Bioconda for Linux and macOS (x86_64, aarch64)