pysam SAM BAM Summary Starter

Use this skill to read a small SAM, BAM, or CRAM file with pysam, summarize core alignment statistics, and optionally emit an indexed BAM artifact for downstream debugging or demos.

What it does

• Opens a local alignment file with pysam.AlignmentFile.
• Reports header references, mapped and unmapped counts, pairing flags, and per-reference mapped counts.
• Optionally writes a BAM copy and builds a .bai index.

When to use it

• You need a deterministic starter for SAM/BAM/CRAM handling in Python.
• You want a tiny verified example of format conversion plus indexing.
• You need a compact JSON summary before building larger alignment-processing skills.

Example

slurm/envs/genomics/bin/python skills/genomics/pysam-sam-bam-summary-starter/scripts/run_pysam_sam_bam_summary.py \
  --input skills/genomics/pysam-sam-bam-summary-starter/examples/toy_reads.sam \
  --out scratch/genomics/pysam_summary.json \
  --bam-out scratch/genomics/toy_reads.bam

Verification

• Skill-local tests: python3 -m unittest discover -s skills/genomics/pysam-sam-bam-summary-starter/tests -p 'test_*.py'
• Expected summary: record_count == 4, mapped_count == 3, and reference_mapped_counts.chr1 == 2