update changelog for v0.1.0

Author: ayobi

CHANGELOG.md

@@ -10,4 +10,17 @@ The format is based on Keep a Changelog, and this project follows Semantic Versi
 ### Added
 - Initial release of ITSxRust.
 - `extract` command for ITS region extraction using HMMER tblout anchors.
-- Deterministic test fixtures and CI checks (fmt, clippy, tests).
+- 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).