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Allow Variant to ReferenceRegion conversion #768

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arahuja opened this Issue Aug 11, 2015 · 1 comment

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arahuja commented Aug 11, 2015

Right now there is no conversion from Variant to ReferenceRegion. This would be needed to perform a RegionJoin with an RDD of Variants. I can add this, but wanted to make sure I wasn't missing in anything, or if there some relationship between Feature and Variant that would take care of this.

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fnothaft Aug 11, 2015

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I see that we have one for Variant to ReferencePosition: https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/models/VariantContext.scala#L49

Since ReferencePosition extends ReferenceRegion, you could use that for a region join. That being said, the Variant -> ReferencePosition mapping assumes all variants are point variants, which isn't the best. Perhaps that is something that should be refactored?

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fnothaft commented Aug 11, 2015

I see that we have one for Variant to ReferencePosition: https://github.com/bigdatagenomics/adam/blob/master/adam-core/src/main/scala/org/bdgenomics/adam/models/VariantContext.scala#L49

Since ReferencePosition extends ReferenceRegion, you could use that for a region join. That being said, the Variant -> ReferencePosition mapping assumes all variants are point variants, which isn't the best. Perhaps that is something that should be refactored?

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 6, 2016

[ADAM-768] ReferenceRegion from variant/genotypes
Resolves #768. Adds apply methods to ReferenceRegion for Avro variant and
genotype records.

@heuermh heuermh closed this in d39b374 Jul 6, 2016

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