Skip to content

CHANGELOG.md

Latest commit

 

History

History
116 lines (98 loc) · 5.88 KB

CHANGELOG.md

File metadata and controls

116 lines (98 loc) · 5.88 KB
Raw

Changelog

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

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

When cargo release runs it promotes the [Unreleased] section below to a versioned entry stamped with the release date; new entries should go under [Unreleased] between releases.

Unreleased

Added

  • chelae detect subcommand: identifies the 3' adapter sequence(s) present in one or two FASTQ files by sampling a modest number of records.
    • Paired-end input discovers adapters via R1/R2 overlap detection (no kit knowledge required) and builds a position-by-position consensus across reads that landed in the same near-identical k-mer cluster.
    • Single-end input scores each read against every built-in kit adapter plus any user --adapter-sequence / --adapter-fasta candidate.
    • 3'-end cleanups (poly-G default-on at min run 10; poly-X A/C/T default-on at min run 5; cut-right quality trim default-on at 4:20) are applied to every read before the overlap probe / candidate scan, so 2-color chemistry artifacts and quality-degraded tails don't corrupt detection. All three can be tuned or disabled (0 for the homopolymer flags, off/none/no for the quality flag).
    • Sampling stops once --num-detections usable detections (default 5000) or --max-reads records (default 1M) are reached. A --min-detections-for-report floor (default 20) refuses to report on samples too small to be informative.
    • Console report is two sections: matched kit(s) with their published adapter sequences, and the full-length discovered consensus per mate with uppercase marking the kit-stable region and lowercase marking any per-sample extension (typically an i7/i5 barcode tail).
    • Per-position consensus uses a discontinuity-aware cut: a running-min baseline of the per-column majority fraction stops the consensus at the first sharp drop, at an absolute floor of 50% majority, or at the column coverage floor — whichever comes first. This prevents plurality-noise bases (e.g. an imbalanced sample-index pool where one index dominates at 25%) from being emitted as if they were real.
    • Optional --output-fasta writes a cross-sample-portable FASTA: when a discovered sequence matches a known kit (within 1 mismatch over the first 16 bp), the kit's full published adapter is emitted in place of the sample-specific consensus, so the FASTA round-trips cleanly through chelae trim --adapter-fasta on every sample in a batch. .gz- extensioned output paths are transparently gzip-compressed. If any mate (PE) or candidate (SE) fails to clear --min-fraction, detect hard-fails with an actionable error rather than writing a silently incomplete FASTA.

Fixed

  • chelae trim --expected-insert-size is now honored. The hint is stored in I-space (insert size) rather than shift-space, so it takes effect on the first pair regardless of variable read length, and --insert-size-stats reports anchor against the same I-space estimate.

Internal

  • BUFFER_SIZE and the FASTQ-reader opening helper are now shared between chelae trim and chelae detect via commands/utils.rs.
  • The benchmark pipeline gained a trim-galore-rs tool wrapper.

0.1.0 - 2026-05-13

Added

  • Initial public release of chelae.
  • chelae trim subcommand: single-pass short-read FASTQ trimming and filtering for SE and PE input.
    • Poly-G 3' trim (on by default).
    • Paired-end overlap-based adapter detection (on by default for PE), plus 3' adapter trimming by user-supplied sequence (--adapter-sequence), FASTA (--adapter-fasta), and built-in kit presets (--kit: truseq, nextera, small-rna, aviti, mgi/dnbseq, and all).
    • Read-structure based hard-trim and UMI extraction (--read-structures), applied after adapter trim so tail-skip segments operate on the cleaned template.
    • Optional poly-X 3' trim (--trim-polyx).
    • Optional 5'→3' and 3'→5' sliding-window quality trimming.
    • Length filter, N-base filter, mean-quality filter, and low-quality-fraction filter.
    • BGZF-compressed FASTQ output.
    • Optional fastp-compatible JSON report (--json) consumed by MultiQC's fastp module unchanged.
    • Optional paired-end insert-size histogram (--insert-size-stats), fastp-shape.
  • Portable SIMD kernels (via the wide crate) for adapter detection, overlap detection, poly-X trim, and sliding-window quality trim.
  • x86_64 release binaries packaged via cargo-multivers with three CPU variants (x86-64, x86-64-v2, x86-64-v4) and runtime dispatch.
  • aarch64 release binaries as a single generic ARMv8-A / NEON build.

Fixed

  • Usage line now always reads Usage: chelae .... clap derives the displayed program name from argv[0]'s basename when bin_name is unset; the cargo-multivers fexecve/memfd launcher passes /proc/self/fd/N as argv[0] under binfmt emulation (e.g. an amd64 biocontainer running on Apple Silicon), so the usage line printed Usage: 11 ... in that environment. Fixed by setting name/bin_name = "chelae" explicitly on the CLI. Also pinned cargo-multivers to >=0.12.0 (the release carrying the fexecve/memfd fix) in the benchmark pipeline installer. Mirrors fulcrumgenomics/riker#38.

Origin

chelae was extracted from fqtk on 2026-04-21; the entire chelae trim implementation was developed as fqtk trim on the tf_trim branch and split into this standalone crate. The pre-split incremental history (design decisions, performance work, benchmarks) lives in the fqtk repo.