BC genomic-coordinates
Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches before they corrupt an analysis. Used whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include "off by one", "0-based", "1-based", "half-open", "coordinate system", "left-align", "normalize variant", "bcftools norm", "chr prefix", "wrong genome build", "liftover", "REF mismatch", and "HGVS".
Converts genomic intervals between coordinate conventions, normalises and compares variant representations, and detects assembly or contig-naming mismatches…
As a process C 59/100 · Has gaps — weak spots: result and completion, inputs and preconditions, failures and branches
What is at stake
Medium-severity findings: the skill is probably honest, but read what alarmed the scanner.
Below is the worst case for this category. The finding here is medium: the guard saw a sign, not a proof.
The skill asks for more than the task needs: broad tool access, credential environment variables, binaries. Every extra permission widens the damage from a mistake or a compromise.
Narrow allowed-tools and the variable list to the minimum; replace binaries with readable sources or scripts.
How to improve
- Your own cases (evals/evals.json, 4–6 real requests with expected answers): the full check would then run those instead of a model-drafted suite.
- A spec.yaml with trigger phrases and assertions — a behaviour contract for CI; `skilltest init` writes a template.
Guard findings · 1
✓ No critical or high findings
Medium and low: 1
-
medium Broad scope
meta-broad-allowed-toolsSKILL.md:1Broad tool permissions pre-approved: Bashallowed-tools: Read Write Edit Bash
Files scanned: 10. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
✓ No remarks against the Agent Skills spec
Process rating: all ten parameters 59/100
- 0Result and completion. Does not say what the result is
- 0Inputs and preconditions. Does not say what the process needs to start
- 0Failures and branches. Linear process with no failure handling
- 30Running it twice. 2 mutating operations with no state check
- 70When it triggers. States when to use, but not when not to
- 100Tools and files. Tools declared in frontmatter
- 100Steps. 4 steps
- 100Consistency. Name and required fields are in place
- 100Execution cost. Instruction body is 2836 tokens
- 100Progress reporting. Reports progress
- low 12 top-level sections: this looks like several domains in one skill
Everything here is measured from the skill text rather than judged by a model, so the numbers are checkable. A parameter weighs more when it is a more common reason for the process to stall.
Quality signals
- +4Description does not say when NOT to use the skill (false activations)
- +3Description length 924: 120–800 characters recommended
- +3Output format is not stated: the model decides each time
- -31 of 5 scripts are never mentioned in SKILL.md
- +2Single-language instructions
- +5Description quotes 12 example trigger phrases
- +4Structure: 13 headings
- +3Step-by-step instructions: 4 items
- +4Has examples (8 code blocks)
- +4Reference files are cited in the instructions (4 of 4)
- +1License stated
Quality base 70; lint remarks subtract, signals add up to 100. Result: 88.