VariantContextConverter never returns DatabaseVariantAnnotation #1097

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akmorrow13 opened this Issue Jul 31, 2016 · 1 comment

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akmorrow13 commented Jul 31, 2016

in VariantContextConverter function convert line 184:
def convert(vc: HtsjdkVariantContext): Seq[ADAMVariantContext]

always creates ADAMVariantContext without a DatabaseVariantAnnotation, even in the 1000genomes files with alleleFrequency fields.

@fnothaft fnothaft added the duplicate label Aug 1, 2016

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fnothaft Aug 1, 2016

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That's going to be patched by #1078. If you need this right now with the ADAM 0.19.0 DatabaseVariantAnnotation schema, you may want to use some derivative upon bigdatagenomics/quinine@a5cb6b0. I'm going to close this as a dupe for now, but please reopen this if you think it should fall outside of #1078.

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fnothaft commented Aug 1, 2016

That's going to be patched by #1078. If you need this right now with the ADAM 0.19.0 DatabaseVariantAnnotation schema, you may want to use some derivative upon bigdatagenomics/quinine@a5cb6b0. I'm going to close this as a dupe for now, but please reopen this if you think it should fall outside of #1078.

@fnothaft fnothaft closed this Aug 1, 2016

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