Need a way for users to add VCF header lines #1233
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fnothaft
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Nov 11, 2016
Resolves bigdatagenomics#1233. Adds a `headerLines` field to all Variant-related GenomicRDDs. In the current implementation, this field is populated by the set of all header lines for all INFO/FORMAT fields that we support. In a future patch, we will also store the header lines that correspond to fields that do not map to a specific field in the Variant/Genotype schema, and that are stored in an attribute map.
fnothaft
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Nov 18, 2016
Resolves bigdatagenomics#1233. Adds a `headerLines` field to all Variant-related GenomicRDDs. In the current implementation, this field is populated by the set of all header lines for all INFO/FORMAT fields that we support. In a future patch, we will also store the header lines that correspond to fields that do not map to a specific field in the Variant/Genotype schema, and that are stored in an attribute map.
heuermh
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Nov 18, 2016
Resolves #1233. Adds a `headerLines` field to all Variant-related GenomicRDDs. In the current implementation, this field is populated by the set of all header lines for all INFO/FORMAT fields that we support. In a future patch, we will also store the header lines that correspond to fields that do not map to a specific field in the Variant/Genotype schema, and that are stored in an attribute map.
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I've kinda known this to be a problem for a while, but I was just using a VCF I saved with ADAM that had genotype filters (
FTfield) in a downstream tool, and I got an exception in the downstream tool because my VCF did not have a##FILTER=<ID=ID,Description="description">line in the header. I have a general idea for how to do this; will post next week for discussion when I'm not bandwidth limited. I think this approach would also work for SAM program fields, which would be a plus.The text was updated successfully, but these errors were encountered: