galaxyproject / galaxyproject/sequence_utils
Enhancement request: enable use with VCFv4.2
- Dominant language
- Python
- Stars
- 6
- Forks
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- Avg merge
- 4h 37m
- Merged PRs (30d)
- 1
Description
https://github.com/galaxyproject/sequence_utils/blob/3112094fbc0c9b7fc13bb318a47216d11c65ca95/galaxy_utils/sequence/vcf.py#L63-L64
VCFv4.0 == ok
VCFv4.1 == ok
VCFv4.2 == tool fails with
https://usegalaxy.org/u/jen-galaxyproject/h/test-vcftomafcustomtrack1
```
Traceback (most recent call last):
File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/vcf_to_maf_customtrack.py", line 192, in
main()
File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/vcf_to_maf_customtrack.py", line 108, in main
vcf_files.append(PopulationVCFParser(galaxy_utils.sequence.vcf.Reader(open(filename)), pop_name))
File "/usr/local/lib/python3.7/site-packages/galaxy_utils/sequence/vcf.py", line 111, in __init__
self.vcf_class = VariantCall.get_class_by_format(metadata_value)
File "/usr/local/lib/python3.7/site-packages/galaxy_utils/sequence/vcf.py", line 15, in get_class_by_format
assert format in VCF_FORMATS, 'Unknown format type specified: %s' % format
AssertionError: Unknown format type specified: VCFv4.2
```
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