Comments (2)
JackCurragh
commented on June 5, 2024
1
Ah yes that makes a lot more sense than arrow.. not sure what I was thinking when I wrote that!
Thank you for your response. I will have to find a way to sanitise the BAMs beforehand I guess!
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GarrettNg
commented on June 5, 2024
Hi Jack,
Thanks for your interest in oxbow.
The InvalidReferenceSequenceName error is coming from our upstream dependency noodles which is reading/parsing the bam file. It looks like you're right that the brackets in the reference name are causing an issue. The name parsing happens in noodles here. noodles is aiming for compliance with file format specs (sam spec page 3 section 1.2.1) and errors out on this kind of thing.
Unfortunately, we don't have a way of handling nonconformant data with oxbow at the moment.
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Related Issues (14)
- Add support for reading extra tags from a BAM file. HOT 1
- pyoxbow: test suite HOT 1
- pyoxbow: sphinx API docs HOT 1
- oxbow: column selection HOT 1
- oxbow: nested field translation
- Reading VCF files? HOT 4
- Byte range mapping API
- Range query API
- Remote file access HOT 1
- Feature request: Return iterator of RecordBatches (in Python)
- read_bam shouldn't require BAM index
- Needs a logo HOT 1
- r-oxbow installation fails HOT 5
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