Versioned security assessment

Report ID: SA-799B8563

6/30/2026, 5:52:00 AM

pysam security assessment v5

Skill Security Certification Report

Audit History
Audit model: codex Historical report
Skill name
pysam
Version
v5
Maintainer
K-Dense-AI
Source
github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pysam
Coverage
6 Files scanned · 2,032 Lines analyzed
Policy version
Unavailable

Highest confirmed finding severity

Medium

4 confirmed security findings require attention.

Installation context

Historical evidence

This report may not describe the currently installable artifact. Open the current Skill page for install guidance.

Open current Skill page

This report does not block or authorize the manifest or ZIP.

Static analysis reported critical and high findings for network access, Windows SAM credentials, weak cryptography, and command execution. Manual review found those severe alerts are false positives caused by genomics terminology, markdown examples, and pysam local fetch() calls. The remaining publication risk is medium because the skill legitimately documents local file writes and pysam wrappers around samtools and bcftools.

Report position

Historical report

Open audit history before using this report to install.

Audit attestation

Not attestable

The required immutable binding is incomplete.

Human verification

Not verified

No human verification is recorded for this report.

Coverage

6 Files scanned · 2,032 Lines analyzed

5 items shown for review

Limitations

This report does not claim runtime or sandbox execution and does not prove the absence of side effects.

Evidence chain

Follow the evidence from source binding to the install contract. Available evidence supports verification; it is not a safety guarantee.

  1. Source

    Binding unavailable

  2. Artifact

    Identity incomplete

  3. Audit

    Complete

  4. Install contract

    Open manifest to verify

    Open manifest

Capabilities observed

Observed means this report recorded supporting evidence. Not recorded does not prove that a capability is absent.

Contains scripts

May execute code included with the Skill.

Not recorded by this audit

Network access

May connect to external services.

Not recorded by this audit

Filesystem access

May read or write local files.

Observed in 4 evidence locations

Env variables

May read values from the process environment.

Not recorded by this audit

External commands

May invoke commands or programs outside the Skill.

Observed in 3 evidence locations

Capability review items (1)
Medium
references/alignment_files.md:17-25references/common_workflows.md:306-328references/sequence_files.md:201-216references/variant_files.md:327-348
Local Genomic File Read and Write Examples
The skill includes examples that open, read, write, convert, index, and summarize local genomic files. This is core pysam behavior, but users should review output paths because examples can overwrite or generate BAM, VCF, FASTQ, FASTA, and CSV files.
The cited examples use local file handles and output writers. The risk is limited to expected filesystem effects in user-directed genomic workflows.

Risk findings

Confirmed security concerns are separated from items that still need review.

Confirmed security concerns (4)

RISK-001 Medium
SKILL.md:213-228references/alignment_files.md:256-264references/variant_files.md:255-269
External Bioinformatics Command Wrappers
The skill documents pysam.samtools and pysam.bcftools wrappers for sorting, indexing, viewing, and converting genomic files. This is expected for a pysam skill and I found no shell-string construction or credential access, but generated workflows can execute local bioinformatics tools and create output files.
The referenced lines directly show pysam.samtools and pysam.bcftools calls. Confidence is high that external tool wrappers are present, while malicious intent is not shown.
RISK-002 Low
SKILL.md:13references/alignment_files.md:1-5
Dismissed Windows SAM Credential Database Alerts
The static scanner treated SAM as the Windows Security Accounts Manager database. In this skill, SAM means Sequence Alignment/Map, a standard genomics alignment format used with BAM and CRAM; no Windows credential database access was found.
The surrounding context explicitly describes genomic alignment files. I found no evidence of Windows system file paths, registry access, or credential extraction.
RISK-003 Low
references/alignment_files.md:56-79references/sequence_files.md:49-65references/variant_files.md:59-73
Dismissed Fetch Network Alerts
The static scanner interpreted fetch() as a network Fetch API call. In these files, fetch() is a pysam method for retrieving local genomic regions from indexed alignment, sequence, variant, or tabix files.
The cited sections define fetch() using genomic coordinates and local file indexes. No HTTP request construction or remote endpoint use appears in those contexts.
RISK-004 Low
SKILL.md:262-265
External Documentation and Platform Links
The skill includes a link to official pysam documentation and a suggestion to consider K-Dense Web for complex workflows. These are outbound references and promotional guidance, but I found no automatic network call, telemetry, or data exfiltration behavior.
The lines are visible documentation text rather than executable code. The confidence is lower because marketplace policy may still require review of promotional guidance.

Expert evidence

Immutable subject identity, scanner metadata, dismissed matches, and source-level evidence.

Artifact subject

Marketplace commit
Unavailable
Content hash
Unavailable
Tree hash
Unavailable
Skill path
Unavailable
Audit payload hash
Unavailable

Analysis metadata

Audit model: codex

Analysis state: Complete

Scope is limited to the recorded files, lines, methods, and evidence. No runtime or sandbox execution is claimed.

Static false positives ignored (1)
Low
SKILL.md:159-170references/alignment_files.md:128-139references/variant_files.md:161-167
Dismissed Markdown Backtick and Weak Crypto Alerts
Many command-execution alerts came from markdown code fences and inline code formatting, not executable Ruby or shell backticks. Weak-crypto alerts did not map to cryptographic operations; the reviewed lines discuss genomic file modes, coordinates, CIGAR operations, and VCF header fields.
The referenced contexts are documentation examples and genomics terminology. I did not find evidence of hashing, encryption, password handling, or dynamic command execution at these locations.

Verify and export

JSON report CITATION.cff SARIF 2.1.0 Signed installation manifest

The manifest and lockfile bind install artifacts to cryptographic hashes. This integrity claim is separate from the security assessment.

Audit attestation: not_attestable