Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add ma-compbio-lab/SkillFoundry --skill pysam-sam-bam-summary-startergit clone --depth 1 https://github.com/ma-compbio-lab/SkillFoundryWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/pysam-sam-bam-summary-starter)<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/pysam-sam-bam-summary-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/pysam-sam-bam-summary-starter/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/ma-compbio-lab/skillfoundry/pysam-sam-bam-summary-starter"><img src="https://agentmods.dev/badge/skills/ma-compbio-lab/skillfoundry/pysam-sam-bam-summary-starter.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00000 | $0.00313 |
| Opus 5 | $0.00000 | $0.00156 |
| Sonnet 5 | $0.00000 | $0.00063 |
| Haiku 4.5 | $0.00000 | $0.00031 |
Grade A, and why
pysam-sam-bam-summary-starter scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
What it actually says
pysam SAM BAM Summary Starter
Use this skill to read a small SAM, BAM, or CRAM file with pysam, summarize core alignment statistics, and optionally emit an indexed BAM artifact for downstream debugging or demos.
What it does
- Opens a local alignment file with
pysam.AlignmentFile. - Reports header references, mapped and unmapped counts, pairing flags, and per-reference mapped counts.
- Optionally writes a BAM copy and builds a
.baiindex.
When to use it
- You need a deterministic starter for
SAM/BAM/CRAMhandling in Python. - You want a tiny verified example of format conversion plus indexing.
- You need a compact JSON summary before building larger alignment-processing skills.
Example
slurm/envs/genomics/bin/python skills/genomics/pysam-sam-bam-summary-starter/scripts/run_pysam_sam_bam_summary.py \
--input skills/genomics/pysam-sam-bam-summary-starter/examples/toy_reads.sam \
--out scratch/genomics/pysam_summary.json \
--bam-out scratch/genomics/toy_reads.bam
Verification
- Skill-local tests:
python3 -m unittest discover -s skills/genomics/pysam-sam-bam-summary-starter/tests -p 'test_*.py' - Expected summary:
record_count == 4,mapped_count == 3, andreference_mapped_counts.chr1 == 2
What ships with it
7 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 7d ago First seen · 30 lines · 0 tokens per session scan A 013667783f05
pysam-sam-bam-summary-starter is a skill published in the GitHub repository ma-compbio-lab/SkillFoundry (39 stars, last pushed 4mo ago), licensed Apache-2.0. It costs nothing until one of its globs matches a file; then it loads 313 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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