pysam
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
Independent static run, no language model, over the same files as the Cisco scan above. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
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.
- Package
- 14 files, 151 KB
- SKILL.md
- 1539 words, 12+ sections
- Code
- Python (4)
- Allowed tools
ReadWriteEditBash- License
- MIT
- Compatibility
- Requires Python 3.9+ and pysam 0.24.1. Bundled scripts use local files. CRAM decoding may require the matching reference FASTA or an explicitly configured REF_PATH/REF_CACHE.
SKILL.md covers: pysam · Overview · Installation · First Decide · Bundled Scripts · Coordinate Contract · The same 100 bases: · Alignment Files · Variant Files · FASTA, FASTQ, and Tabix · CRAM, Remote I/O, and Threads · Wrapped samtools and bcftools
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
SKILL.md | doc | 13 KB |
references/alignment_files.md | doc | 13 KB |
references/api_reference.md | doc | 10 KB |
references/common_workflows.md | doc | 14 KB |
references/coordinates_and_indexing.md | doc | 8.8 KB |
references/cram_and_performance.md | doc | 9.4 KB |
references/migration_to_0_24.md | doc | 5.4 KB |
references/sequence_files.md | doc | 9.3 KB |
references/sources.md | doc | 7.5 KB |
references/variant_files.md | doc | 12 KB |
scripts/alignment_qc.py | script | 11 KB |
scripts/filter_alignments.py | script | 12 KB |
scripts/inspect_hts.py | script | 14 KB |
scripts/variant_summary.py | script | 12 KB |
External hosts referenced
pysam.readthedocs.io samtools.github.io www.htslib.org github.com arxiv.org doi.org export.arxiv.org pypi.org
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Environment variables referenced
REF_PATH
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-pysam-scan.json
- Badge for your README:
- Request a re-scan