Changelog

All notable changes to this project will be documented in this file.

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

[Unreleased]

Initial release of ITSxRust.
extract command for ITS region extraction using HMMER tblout anchors.
Platform presets: --preset ont and --preset hifi with tuned E-values, length constraints, and confidence thresholds.
Partial-chain fallback: recover subregions from 2-anchor pairs when the full 4-anchor chain is unavailable.
Confidence classification: reads labelled confident, ambiguous, or partial based on per-anchor score/E-value thresholds.
--write-ambiguous and --write-skipped flags to divert reads to separate files.
Exact dereplication (--derep): hash identical sequences and search only unique representatives, projecting results back to duplicates.
Multi-region output: --region all extracts ITS1, ITS2, and full ITS simultaneously, treating --output as a prefix.
FASTQ support with quality score preservation; gzipped input support.
--qc-json for per-sample QC summary (read counts, skip-reason breakdown, parameters).
--anchors-tsv and --anchors-jsonl for per-read anchor coordinates and confidence labels.
--explain N diagnostic flag for inspecting skip reasons.
--tblout-existing to reuse a previous nhmmer tblout file.
Docker image with bundled HMMER.
Bioconda recipe.
Deterministic test fixtures and CI checks (fmt, clippy, tests).