#moonbit-fastq-qc

moonbit-fastq-qc is a MoonBit Native toolkit for validating FASTQ data, measuring read quality, and preparing reads for local analysis pipelines. It accepts plain FASTQ and FASTQ.GZ input and writes deterministic JSON and standalone HTML reports.

#Capabilities

FASTQ structure, DNA alphabet, sequence/quality length, and truncation checks
Phred+33 and Phred+64 quality handling
Read length, GC, N content, per-position quality, duplication, and adapter metrics
Optional length, quality, N-count, and N-ratio filtering
Adapter, fixed-length, and low-quality-tail trimming
Paired-end name, duplicate, and length consistency checks
Native gzip input through the bundled zlib adapter
Versioned JSON output and offline HTML output

The repository contains synthetic fixtures only. It does not contain clinical, patient, or production sequencing data.

#Quick start

moon run --target native cmd/fastq_qc -- fixtures/basic.fastq \
  --phred-offset 33 \
  --adapter-file fixtures/adapters.txt \
  --json _build/report.json \
  --html _build/report.html

Gzip input uses the same command with fixtures/basic.fastq.gz. The JSON report is the machine-readable contract; HTML embeds the same report and does not request network resources.

#Library layout

fastq/             validated record model and parser
metrics/           quality, length, GC, and N statistics
contamination/     adapter and duplicate analysis
pipeline/          deterministic filtering and trimming
paired/            paired-end consistency checks
report/            versioned JSON and standalone HTML renderers
native/gzip/       Native gzip bridge and its third-party notices
cmd/fastq_qc/      command-line wiring and file I/O
fixtures/          synthetic, checksummed examples
scripts/            reproducible source-scale and benchmark commands
docs/               validation notes and fixture documentation

#Development

Install the current stable MoonBit toolchain using the official installer, then run:

moon fmt --check
moon check --deny-warn
moon info
git diff --exit-code
moon test --deny-warn
moon test --target native --deny-warn

For a transparent source-size breakdown on Windows:

powershell -ExecutionPolicy Bypass -File scripts/source_scale.ps1

The script reports project MoonBit production/test lines, project-owned Native lines, and bundled third-party zlib lines separately. Generated _build files, interface files, documentation, and third-party code are not silently mixed into the MoonBit total.

#Reproducibility and limitations

Fixtures and their hashes are documented in fixtures/README.md. The validation matrix and observed local measurements are recorded in docs/validation.md. Benchmark numbers are machine- and toolchain-dependent observations, not performance guarantees.

This project is intentionally smaller than a full FastQC replacement. It does not provide remote input, clinical interpretation, complete FastQC module compatibility, or automatic repair of inconsistent paired-end data.