The Agent Skills Directory

[COMMAND_EXECUTION]: The skill utilizes the pysam library to execute external bioinformatics command-line tools, specifically samtools and bcftools (e.g., pysam.samtools.sort and pysam.bcftools.view as documented in SKILL.md). This is a core feature for performing genomic analysis tasks.
[PROMPT_INJECTION]: The skill presents an indirect prompt injection surface due to its handling of external genomic data files. * Ingestion points: External data is loaded using pysam.AlignmentFile, pysam.VariantFile, pysam.FastaFile, pysam.FastxFile, and pysam.TabixFile as described across the reference documentation. * Boundary markers: The provided examples do not demonstrate the use of delimiters or specific instructions to the agent to ignore potential commands embedded within data fields. * Capability inventory: The skill possesses the ability to read and write files, as well as execute external bioinformatics commands through the pysam interface. * Sanitization: The provided documentation and code snippets do not show explicit sanitization or validation steps for the content of the genomic files before processing.
[EXTERNAL_DOWNLOADS]: The skill's setup instructions include downloading the pysam package from the official Python Package Index (PyPI) via uv pip install pysam. This is a standard dependency for a well-known bioinformatics library.

pysam