F/mixed ploidy genotype array #171
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…p#169 This decodes non-allele values aka padding to -2 for mixed ploidy data when using the Genotypes.array() method. Previously non-alleles would overflow to -1 making lower ploidy genotypes indistinguishable from partial genotypes of a higher ploidy.
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thank you. i have tagged this as v0.20.7 and uploaded to pypi. it will automatically build on bioconda shortly and should be available there in a few hours. |
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Awesome, thanks @brentp ! |
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Hi @brentp I finally got around to trying v0.20.7 installed from PyPI with It looks like |
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Ok. I think it should work as v0.20.8 from pypi now. Thanks for letting me know. |
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Great v0.20.8 is working correctly, thanks again! |
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This fixes #169 by always using the value
-2to indicate non-alleles (i.e. padding) in a mixed-ploidy genotype array.As mentioned in the issue I can make this value configurable if that is preferred.
I also added a test using an existing VCF though I think that the
.value used for the first sample in the fourth variant is technically not within standard because there should be a value for each format field.