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gtars skill

by K-Dense-AI·K-Dense-AI/scientific-agent-skills·47k stars·MIT

Use Gtars for local genomic interval models and set algebra, overlaps and counts, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and the CLI.

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Clean: nothing in its files matched our rules. We read 15 files in the folder on 2026-09-28.

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Install the gtars skill

A skill is a folder. Copy it into your agent's skills folder and the agent loads it when the task matches its description. 

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills
mkdir -p ~/.claude/skills
cp -r /tmp/scientific-agent-skills/skills/gtars ~/.claude/skills/gtars
available in every project

In the Claude apps, zip the folder and upload it from the Skills settings. The folder on GitHub

The instructions your agent would load

SKILL.md as published, without the frontmatter. Read it on GitHub

Gtars

Gtars provides native Rust implementations, Python bindings, and a feature-gated gtars binary for genomic interval and reference-sequence work. Start with the bundled local inspectors; call upstream code only after the data contract, provenance, resource bounds, and side effects are explicit.

Verified snapshot (2026-07-23)

2026-06-17, Requires-Python >=3.10.

  • Python: gtars==0.9.2, released

2026-06-15. Its default feature set is empty.

  • Rust meta-crate: gtars=0.9.0, released

the installed binary is named gtars.

  • CLI crate/binary: gtars-cli=0.9.0;

released 2026-06-17. gtars=0.9.0 itself pins its component release set, which includes refget 0.9.0.

  • Direct refget crate: gtars-refget=0.9.1,

independently. Do not assume matching numbers mean matching artifacts.

  • Upstream intentionally versions workspace crates, Python bindings, and CLI

against the 0.9.2 Python stubs/runtime and the v0.9.0 CLI/Rust source.

  • The published docs changelog stops at 0.5.1. API examples here were checked

The license: MIT field covers this skill. Published gtars crates declare MIT, while the GitHub repository currently displays BSD-2-Clause at the root; verify the exact artifact's license before redistribution.

Native-code trust gate and exact pins

The Python wheel contains a PyO3 native extension. Cargo installation compiles a native binary and can run dependency build scripts. Treat either path as code execution:

GitHub's v0.9.0 binary release includes per-archive .sha256 sidecars.

  1. Confirm the official PyPI/crates.io/GitHub owner and immutable version.
  2. Review filenames, platform tags, release provenance, license, and SHA-256.

or archive installer. Use isolation and CPU/RAM/disk/time limits.

  1. Never run an untrusted prebuilt binary, wheel, source tree, Cargo build script,
  1. Keep a lockfile and artifact hashes with the analysis manifest.

After that review, create an isolated Python environment:

uv venv --python 3.11 .venv-gtars
uv pip install --dry-run --python .venv-gtars/bin/python "gtars==0.9.2"
uv pip install --python .venv-gtars/bin/python "gtars==0.9.2"
.venv-gtars/bin/python -c \
  "import gtars; assert gtars.__version__ == '0.9.2'; print(gtars.__version__)"

For the reviewed CLI source release:

cargo install gtars-cli --version 0.9.0 --locked
gtars --version
gtars --help

For a Rust project, pin the wrapper exactly and enable only required features:

[dependencies]
gtars = { version = "=0.9.0", default-features = false, features = [
  "core", "overlaprs", "uniwig", "tokenizers", "refget"
] }

Use gtars-refget = "=0.9.1" directly only when the newer direct component API is required and compatibility has been tested. Do not replace these pins with a Git branch or an unreviewed release.

Genomic data contract

Apply this contract before every operation:

Require 0 <= start < end <= contig_length. Gtars coordinates are u32, so reject values above 4,294,967,295.

  1. Coordinates: BED intervals are 0-based and half-open: [start, end).

chromosome-sizes or refget sequence-collection metadata. Never infer assembly from filenames or chr prefixes.

  1. Assembly: record an assembly accession/version and the SHA-256 of the exact

mitochondrial aliases are not interchangeable. Rename or liftover only as a separately reviewed transformation.

  1. Contigs: compare names exactly. 1 and chr1, alternate loci, decoys, and

order and numeric start/end when the operation requires it. Python RegionSet(path) currently sorts lexicographically by contig and start while loading; do not rely on original row order afterward.

  1. Sorting: preserve the original file, then sort a copy by chromosome-sizes

fields, but a file-backed Python RegionSet currently initializes its separate strands vector to *. Several set operations drop strand. Preserve and validate strand externally when it is scientifically meaningful.

  1. Strand: BED6 uses +, -, or .. Region.rest retains trailing BED

merge overlapping and adjacent intervals; ordinary half-open overlap does not treat [0,10) and [10,20) as overlapping.

  1. Duplicates/adjacency: choose policies explicitly. reduce() and consensus

Run the local validator first:

python3 -B scripts/bed_validator.py \
  --input data.bed.gz \
  --assembly GRCh38.p14 \
  --chrom-sizes GRCh38.p14.chrom.sizes \
  --require-sorted

Safe local workflow

system, strand policy, patient/replicate groups, and intended outputs.

  1. Inventory local files, checksums, assembly, contig dictionary, coordinate

names by guesswork.

  1. Validate BED/fragments and estimate work. Pilot a small synthetic file.
  2. Choose Python, CLI, or Rust from the documented surface; do not translate API

disk, output size, and wall time.

  1. Set hard limits for input bytes/records/files, threads/jobs, memory, temporary

explicitly approved.

  1. Run in a dedicated output directory. Refuse collisions unless overwrite was
  1. Revalidate output sorting, bounds, row counts, checksums, and provenance.

Current Python core

Imports are from submodules, not the gtars top level:

from gtars.models import Region, RegionSet

query = RegionSet.from_regions(
    [
        Region(chr="chr1", start=100, end=200, rest=None),
        Region(chr="chr1", start=300, end=400, rest=None),
    ],
    strands=["+", "-"],
)
universe = RegionSet.from_vectors(
    ["chr1", "chr1"],
    [150, 500],
    [350, 600],
)

counts = query.count_overlaps(universe)       # one count per query region
flags = query.any_overlaps(universe)          # one bool per query region
indices = query.find_overlaps(universe)       # indices into universe
pieces = query.intersect_all(universe)        # all intersection fragments
fraction = query.coverage(universe)           # fraction of query bp covered

RegionSet.sort() mutates and returns None. Set algebra includes reduce, setdiff, pintersect (pairs by index), concat, union, jaccard, coverage, overlapcoefficient, intersectall, closest, cluster, and gaps. Read references/python-api.md before relying on ordering or strand.

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