SACGF / SACGF/variantgrid

'BulkNoGenotypeVCFProcessor' object has no attribute 'get_ref_alt_allele_depth'

Open
#1,865 1 comment 0 reactions 1 assignee Claimed by @davmlaw View on GitHub
Dominant language
Python
Stars
30
Forks
3
Avg merge
9h 22m
Merged PRs (30d)
40

Description

```
UploadPipeline 13692 failed. Filename: VCF Error: 'BulkNoGenotypeVCFProcessor' object has no attribute 'get_ref_alt_allele_depth'
Traceback (most recent call last):
File "/mnt/variantgrid/upload/tasks/vcf/import_vcf_step_task.py", line 88, in run
items_processed = self.process_items(upload_step)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/variantgrid/upload/tasks/vcf/genotype_vcf_tasks.py", line 129, in process_items
return import_vcf_file(upload_step, bulk_inserter)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/mnt/variantgrid/upload/vcf/vcf_import.py", line 444, in import_vcf_file
bulk_inserter.finish()
File "/mnt/variantgrid/upload/vcf/abstract_bulk_vcf_processor.py", line 59, in finish
self._finish()
File "/mnt/variantgrid/upload/vcf/bulk_genotype_vcf_processor.py", line 161, in _finish
self.finished_locus()
File "/mnt/variantgrid/upload/vcf/bulk_genotype_vcf_processor.py", line 373, in finished_locus
self._add_shared_locus_modified_imported_variants()
File "/mnt/variantgrid/upload/vcf/bulk_genotype_vcf_processor.py", line 394, in _add_shared_locus_modified_imported_variants
if not (self.preprocess_vcf_import_info and self.get_ref_alt_allele_depth):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'BulkNoGenotypeVCFProcessor' object has no attribute 'get_ref_alt_allele_depth'. Did you mean: 'get_ref_alt_allele_depth_default'?
```

Contributor guide

No contributing guide indexed for this repository

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.