SACGF / SACGF/variantgrid

VCFBedIntersection broken

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#1,276 0 comments 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
Dominant language
Python
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30
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3
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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