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Changelog

All notable changes to the Fastp Plugin for Geneious Prime will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[1.1.0] - 2025-11-14

Added

  • Command Logging to Info Tab: The exact fastp/fastplong command executed is now saved to the Info tab of output sequence lists
  • Stdout Logging to Info Tab: Standard output from fastp/fastplong is captured and saved to the Info tab
  • Stderr Logging to Info Tab: Standard error output from fastp/fastplong is captured and saved to the Info tab
  • Exit Code Logging: Process exit code is now logged to the Info tab
  • Enhanced Console Logging: Comprehensive logging to terminal for debugging when launching Geneious from command line
  • FastpExecutionResult Class: New result class to encapsulate command, exit code, stdout, and stderr

Changed

  • FastpExecutor: Refactored to return FastpExecutionResult instead of just exit code
  • Sequence List Import: Fixed to import as single sequence list instead of individual sequences
  • SequenceListDocument Support: Added proper handling for SRA imports and other sequence list formats

Fixed

  • SRA Import Support: Plugin now properly handles sequence lists from SRA downloads
  • Document Type Detection: Improved detection of SequenceListDocument vs individual sequences

[1.0.0] - 2025-11-13

Added

  • Initial release of Fastp Plugin for Geneious Prime
  • Integration of fastp v1.0.1 and fastplong v0.4.1
  • Automatic paired-end detection via file naming conventions
  • Automatic read type detection (short <1000bp vs long >=1000bp reads)
  • Universal macOS binaries (Intel x86_64 + Apple Silicon arm64)
  • 40+ configurable parameters with sensible defaults
  • Quality filtering, adapter trimming, length filtering
  • PolyG/PolyX trimming for NextSeq/NovaSeq platforms
  • UMI processing support
  • Comprehensive statistics in Geneious Info tab
  • No external dependencies (binaries bundled)

Implementation

  • 5 Java classes (2,927 lines of production code)
  • FastpPlugin: Plugin registration
  • FastpOperation: Main workflow orchestration
  • FastpOptions: UI with 40+ parameters
  • FastpExecutor: Command execution
  • FastpBinaryManager: Binary management

License

  • Plugin code: MIT License
  • Bundled binaries: fastp and fastplong (both MIT licensed)

Platform Support

  • macOS: Full support (universal binary)
  • Linux/Windows: Planned for future releases