The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill recommends installing the 'pysam' package using 'uv pip install pysam'. This is a standard dependency installation of a well-known bioinformatics library from the official Python Package Index (PyPI).
[COMMAND_EXECUTION]: The skill uses the 'pysam' library's built-in wrappers to execute external bioinformatics utilities such as samtools and bcftools (e.g., 'pysam.samtools.sort', 'pysam.samtools.index', 'pysam.bcftools.view'). These operations are fundamental to the skill's stated purpose of processing sequencing alignment and variant files.
[PROMPT_INJECTION]: The skill features a surface for indirect prompt injection as it is designed to process external genomic data files (BAM, VCF, FASTA, etc.).
Ingestion points: Data is ingested from external files through 'pysam.AlignmentFile', 'pysam.VariantFile', 'pysam.FastaFile', 'pysam.FastxFile', and 'pysam.TabixFile' (e.g., in 'references/alignment_files.md' and 'references/variant_files.md').
Boundary markers: No explicit boundary markers or 'ignore' instructions are provided to the agent when processing these external data sources.
Capability inventory: The skill allows the execution of external bioinformatics commands via 'pysam.samtools' and 'pysam.bcftools', and it can perform file write operations to save results (e.g., in 'SKILL.md' and 'references/common_workflows.md').
Sanitization: The skill does not perform sanitization or content validation on the genomic data before it is read by the agent or passed to processing functions.
[SAFE]: No malicious patterns, obfuscation, or unauthorized data exfiltration were detected. The functionality is consistent with its documentation and intended use-case in genomic data processing.

pysam