[25.0] Skip sam metadata if we have too many references #20820
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This can cause OOM issues.
jmchilton
reviewed
Aug 28, 2025
| ] | ||
| dataset.metadata.sort_order = dataset.metadata.bam_header.get("HD", {}).get("SO", None) | ||
| dataset.metadata.bam_version = dataset.metadata.bam_header.get("HD", {}).get("VN", None) | ||
| with pysam.AlignmentFile(dataset.get_file_name(), mode="rb", check_sq=False) as bam_file: |
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I'm going to approve because your time is valuable and I think you have more important things to work on but I do feel like adding a metadata element to indicate these lists are truncated would be the ideal thing to do in this case so the meaning of these fields is consistent across bam files.
jmchilton
approved these changes
Aug 28, 2025
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This can cause OOM issues.
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