RustQC v0.2.1

Bug fixes

• Fix SIMD builds by scoping rustflags to target triple with explicit --target (#90, #91)

Other changes

• Trigger releases via workflow dispatch instead of tag push (#92)

RustQC v0.1.1

Bug fixes

• Use gene-level stats in featureCounts summary, add biotype summary (#66)
• Include overflow bucket in inner_distance histogram bulk cutoff loop (#67)
• Fix duplicate rna/ segment in sibling page links (#70)

Changes

• Publish to crates.io on release (#62)

Documentation

• Add AI provenance page, streamline benchmarks
• Fix broken internal links by converting absolute to relative paths
• Add Seqera AI to AI provenance page

RustQC v0.1.0

Initial release of RustQC -- fast quality control tools for sequencing data, written in Rust.

A single rustqc rna command runs 15 QC analyses in one pass over the BAM file, producing output that is format- and numerically identical to the upstream tools and fully compatible with MultiQC.

Tools

• dupRadar -- PCR duplicate rate vs. expression analysis with density scatter plots, boxplots, and expression histograms. 14-column duplication matrix with logistic-regression model fitting matching the R dupRadar package.
• featureCounts -- Gene-level read counting with assignment summary, compatible with Subread featureCounts. Includes per-biotype read counting and MultiQC integration.
• RSeQC (8 tools) -- RSeQC-compatible implementations of bam_stat, infer_experiment, read_duplication, read_distribution, junction_annotation, junction_saturation, inner_distance, and TIN (Transcript Integrity Number). Includes native plot generation (PNG + SVG) with no R dependency.
• preseq -- Library complexity extrapolation (lc_extrap) matching preseq v3.2.0, including C++ RNG FFI for reproducible bootstrap sampling.
• Qualimap rnaseq -- Gene body coverage profiling, read genomic origin, junction analysis, and transcript coverage bias matching Qualimap.
• samtools -- flagstat, idxstats, and full stats output (SN section + all histogram sections) matching samtools.

Features

• Single static binary with no runtime dependencies
• SAM, BAM, and CRAM input support (auto-detected)
• Multi-threaded alignment processing with htslib thread pool
• GTF annotation support (gzip-compressed files accepted)
• YAML configuration for output control, chromosome name mapping, and tool parameters
• Multiple BAM file support via positional arguments
• --sample-name flag to override BAM-derived sample name in output filenames
• Per-tool seed flags (--tin-seed, --junction-saturation-seed, --preseq-seed) for reproducible results
• Docker container at ghcr.io/seqeralabs/rustqc
• Cross-platform builds (Linux x86_64/aarch64, macOS x86_64/aarch64)