polars-bio

Fast genomic interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps), multi-format bioinformatics I/O, DataFusion SQL, and pileup on Polars DataFrames via polars-bio. A scalable bioframe/bedtools alternative.

Quality

80%

Does it follow best practices?

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Securityby

Low

Low-risk findings worth noting

Quality

Content

86%Weight 40%Scale 1-5

Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.

The body is actionable and well-structured, with executable commands covering all subcommands and real output examples. Minor conciseness trimming and an explicit error-recovery loop would lift it further.

Dimension	Reasoning	Score
Conciseness	Dense, purposeful body with executable commands and skimmable sections; a few prose blocks ('Why This Exists', performance attribution) could be trimmed but largely earn their place.	4 / 5
Actionability	Full CLI reference with copy-paste-ready commands for every subcommand plus real example outputs (result.json, report.md excerpt), fully executable and covering common cases.	5 / 5
Workflow Clarity	Clear Validate → Run → Open → Demo-fallback sequence with explicit input validation (BED >=4 cols, BAM .bai); falls short of 5 only in lacking an explicit run-failure feedback loop.	4 / 5
Progressive Disclosure	Overview SKILL.md with well-signaled, one-level-deep references to real bundle files (polars_primer.md, file_io.md, etc.); content appropriately split and easy to navigate.	5 / 5
	Total	18 / 20 Passed

Description

75%Weight 40%Scale 1-5

Based on the skill's description, can an agent find and select it at the right time? Clear, specific descriptions lead to better discovery.

The description is highly specific and distinctive, naming concrete operations and a clear niche. Its main weakness is the absence of an explicit 'Use when...' trigger clause, which caps completeness at 3.

Suggestions

Add an explicit 'Use when...' clause with concrete trigger phrases (e.g., 'Use when overlapping, merging, or computing coverage on BED intervals, or running SQL on VCF/BAM').

Include common synonyms such as 'intersect' and key file extensions like '.bed' to improve natural trigger term coverage.

Dimension	Reasoning	Score
Specificity	Lists eight concrete interval operations (overlap, nearest, merge, coverage, cluster, complement, subtract, count-overlaps) plus multi-format I/O, SQL, and pileup — comprehensive, specific actions.	5 / 5
Completeness	Has a clear 'what', but no explicit 'Use when...' trigger clause; per rubric guideline a missing explicit trigger guidance caps completeness at 3.	3 / 5
Trigger Term Quality	Strong natural keywords (overlap, merge, coverage, bioframe, bedtools, pileup, SQL) but missing common synonyms like 'intersect' and file extensions like '.bed'.	4 / 5
Distinctiveness Conflict Risk	Names a distinct genomic niche (interval arithmetic on Polars DataFrames via polars-bio) and positions as a bioframe/bedtools alternative, giving minimal conflict risk.	5 / 5
	Total	17 / 20 Passed

Validation

93%

Warnings & errors only

Checks the skill against the spec for correct structure and formatting. All validation checks must pass before discovery and implementation can be scored.

Validation — 15 / 16 Passed

Validation for skill structure

Criteria	Description	Result
metadata_field	'metadata' should map string keys to string values	Warning

	Total	15 / 16 Passed

Repository: ClawBio/ClawBio
Path: skills/polars-bio/SKILL.md
Commit: 00f070d

Reviewed: 4 days ago

Table of Contents

Discovery Implementation Validation

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