Dev/2.0.0

[Sam-Sims]

[2.0.0] - 2025-08-12

Added

• Added a reads_extracted_per_taxon field to to summary report (paraseq speed up? #28)
• Added a proportion_extracted field to summary report (paraseq speed up? #28)
• Added the version to summary report (paraseq speed up? #28)
• Added an output format (fasta or fastq) field to the summary report (paraseq speed up? #28)
• Added a --verbose flag (in addition to the existing -v)

Changed

• Removed -O for compression type, now uses --compression-format for clarity.
• Removed -l for compression level, now uses --compression-level for clarity.
• Renamed --json-report to --summary
• Improved the JSON report format to make it easier to read by removing Paired and Single fields and instead having a simple total_reads_in and total_reads_out field.

Fixed

• Removed duplicate log message for taxon IDs identified
• Clippy warnings