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To add explicit handling on missing DS in CYVCF2Genotype #112

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liangyy opened this issue Dec 4, 2020 · 0 comments · Fixed by #113
Closed

To add explicit handling on missing DS in CYVCF2Genotype #112

liangyy opened this issue Dec 4, 2020 · 0 comments · Fixed by #113

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@liangyy
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liangyy commented Dec 4, 2020

When user wrongly specified --vcf_mode imputed but there is actually no DS field in VCF, the script will silently exit due to the KeyError exception in the generator at this line:

d = numpy.apply_along_axis(lambda x: x[0], 1, variant.format("DS"))

In order to improve the error messaging, we need to handle the exception explicitly by raising up the error.

@liangyy liangyy mentioned this issue Dec 13, 2020
@liangyy liangyy linked a pull request Dec 13, 2020 that will close this issue
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