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.

SAM/BAM/CRAM Basics

"Read a BAM file" → Open a binary alignment file and iterate over aligned reads with their mapping coordinates, flags, and quality scores.

• Python: pysam.AlignmentFile() (pysam)
• CLI: samtools view (samtools)
• R: scanBam() (Rsamtools)

View and convert alignment files using samtools and pysam.