BC pysam
Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
Provides Python/HTSlib workflows for genomic files.
As a process C 56/100 · 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
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medium Broad scope
meta-broad-allowed-toolsSKILL.md:1Broad tool permissions pre-approved: Bashallowed-tools: Read Write Edit Bash
Files scanned: 14. Evidence is masked. Grey chips explain why severity was lowered.
Against the Agent Skills spec
- note
edit-residuethe text marks something as outdated (lines 308): check that old rules are not kept next to new ones — the full check reads the text for contradictions
Process rating: all ten parameters 56/100
- 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. 4 mutating operations with no state check
- 50When it triggers. No condition that starts the skill
- 100Tools and files. Tools declared in frontmatter
- 100Steps. 36 steps
- 100Consistency. Name and required fields are in place
- 100Execution cost. Instruction body is 3257 tokens
- 100Progress reporting. Reports progress
- low 14 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
- +5Description has no quoted example phrases that should trigger the skill
- +4Description does not say when NOT to use the skill (false activations)
- +3Output format is not stated: the model decides each time
- +2Single-language instructions
- +3Description length 223: enough signal without eating the budget
- +4Structure: 15 headings
- +3Step-by-step instructions: 36 items
- +4Has examples (16 code blocks)
- +4Reference files are cited in the instructions (9 of 9)
- +3All 4 scripts are documented
- +1License stated
Quality base 70; lint remarks subtract, signals add up to 100. Result: 92.