Version Compatibility

Reference examples tested with: pysam 0.22+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Alignment Indexing

Create indices for random access to alignment files using samtools and pysam.

"Index a BAM file" → Create a .bai/.csi index enabling random access to genomic regions.

• CLI: samtools index file.bam
• Python: pysam.index('file.bam')