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Provide mechanism to change types of fields #33

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jeromekelleher opened this issue Feb 23, 2024 · 0 comments
Open

Provide mechanism to change types of fields #33

jeromekelleher opened this issue Feb 23, 2024 · 0 comments
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enhancement New feature or request help wanted Extra attention is needed

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@jeromekelleher
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Some programs don't do a great job of typing or sizing the output VCF fields. E.g., this is some SnpEff output (I think)

##INFO=<ID=GDI-Phred,Number=.,Type=String,Description="Phred-scaled GDI scores">
##INFO=<ID=GDI,Number=.,Type=String,Description="gene damage index score, a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population from doi 1>

This has been marked as String, Number=".", where it probably should be Integer, Number=1.

One way we could do this is to check the correspondence between the VCF types in the VCF metadata with the types in the Zarr schema, and to push that field through a "conversion" code path if they are not compatible. So, here, we'd see that the original VCF type is String and the Zarr type is int, and we'd have to pass the field through an integer parsing code path.

An nice feature to add at some point then would be to take an input Zarr schema and to automatically detect some common mistyped fields and correct them.

@jeromekelleher jeromekelleher added enhancement New feature or request help wanted Extra attention is needed labels Feb 23, 2024
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