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[BQ to VCF] Add the correct number of repeated "null" values #415

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arostamianfar opened this issue Nov 13, 2018 · 0 comments
Open

[BQ to VCF] Add the correct number of repeated "null" values #415

arostamianfar opened this issue Nov 13, 2018 · 0 comments
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@arostamianfar
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Currently, we assign Number=. for repeated INFO/FORMAT fields that are not under alternate_bases (i.e. have Number=A). We output . for any field that is null in the BigQuery table, which is fine according to the spec if the Number is also defined as ..

However, if the user provides a --representative_header_file and the value is null, the spec requires the correct number of .s to be present (e.g. if Number=2, then we should use .,.). This gets a bit tricky for Number=G or Number=R as we need to dynamically calculate the correct number depending on the variant.

For fields that are not null, we can use the same approach to validate that correct number of values are set when outputting the VCF lines too.

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