[vep] Rework VEP with more visibility #9973
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1. Don't ignore parse errors by default. These shouldn't be happening with modern VEP versions anyway (they were caused by genes named NaN or something in older versions) 2. Don't silently drop variants that don't have a match in VEP. All keys coming in will have a row coming out with a VEP annotation (maybe NA) and a partition/block index.
chrisvittal
approved these changes
Feb 2, 2021
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chrisvittal
previously requested changes
Feb 2, 2021
hail/python/hail/methods/qc.py
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| def vep(dataset: Union[Table, MatrixTable], config=None, block_size=1000, name='vep', csq=False): | ||
| csq=bool, | ||
| tolerate_parse_error=bool) | ||
| def vep(dataset: Union[Table, MatrixTable], config=None, block_size=1000, name='vep', csq=False, tolerate_parse_error=False): |
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Missed this first go, keyword only for the new parameter?
chrisvittal
approved these changes
Feb 3, 2021
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with modern VEP versions anyway (they were caused by genes named NaN
or something in older versions)
coming in will have a row coming out with a VEP annotation (maybe NA)
and a partition/block index.