VCFBedIntersection broken
- Dominant language
- Python
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- Avg merge
- 9h 28m
- Merged PRs (30d)
- 42
Description
* VCFBedIntersection is leaving orphaned VariantCollection records - need historical migration and should listen to delete signal
* I don't think we use this anymore, so maybe turn it off via setting?
* Since quite a while (maybe even Python3 switch!?), it has been broken - it's done via signal so we never noticed:
```
File "/data/variantgrid/snpdb/tasks/vcf_bed_file_task.py", line 95, in vcf_bed_intersection_task
write_qs_to_vcf_file_sort_alphabetically(vcf_queryset, text_pipe_in)
File "/data/variantgrid/snpdb/variants_to_vcf.py", line 40, in write_qs_to_vcf_file_sort_alphabetically
return _write_sorted_values_to_vcf_file(header_lines, sorted_values, f, info_dict=info_dict)
File "/data/variantgrid/snpdb/variants_to_vcf.py", line 46, in _write_sorted_values_to_vcf_file
f.write(line_bytes)
TypeError: write() argument must be str, not bytes
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/data/variantgrid/snpdb/tasks/vcf_bed_file_task.py", line 102, in vcf_bed_intersection_task
stderr_output = intercept_bed_pipe.stderr.read()
ValueError: read of closed file
```
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