The Agent Skills Directory

[EXTERNAL_DOWNLOADS]: The skill utilizes the pysam library, which is a standard and well-regarded bioinformatics package. It is installed from the official Python Package Index (PyPI), which is a trusted source for software dependencies.\n- [COMMAND_EXECUTION]: The skill demonstrates the use of the pysam.samtools and pysam.bcftools modules to perform genomic data processing tasks. These operations involve calling standard bioinformatics command-line tools through library wrappers, which is the intended and safe use of this toolkit.\n- [INDIRECT_PROMPT_INJECTION]: The skill is designed to process external genomic files (e.g., BAM, VCF, FASTA). While these represent an external data ingestion surface, the risk of indirect prompt injection is minimal due to the specialized, non-natural-language nature of genomic data formats.\n
Ingestion points: The skill reads genomic data through pysam.AlignmentFile, pysam.VariantFile, and pysam.FastaFile classes.\n
Boundary markers: Not applicable, as the library performs structured parsing of specific binary and text-based genomic formats.\n
Capability inventory: The skill enables file system reads and writes and execution of specialized bioinformatics command-line tool wrappers.\n
Sanitization: Relies on the parsing integrity of the underlying htslib C library used by pysam.

pysam