ReferenceRegion on Genotype seems busted? #1286

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fnothaft opened this Issue Nov 20, 2016 · 0 comments

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fnothaft commented Nov 20, 2016

Looking at the code:

def apply(genotype: Genotype): ReferenceRegion = {
  ReferenceRegion(genotype.getVariant)
}

After 525fda8, we don't set some of the Variant fields in Genotype. I'm curiously concerned as to how we haven't previously caught this?

@fnothaft fnothaft added the bug label Nov 20, 2016

@fnothaft fnothaft added this to the 0.21.0 milestone Nov 20, 2016

@fnothaft fnothaft self-assigned this Nov 20, 2016

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 25, 2016

[ADAM-1286] Fixed ReferenceRegion.apply(genotype: Genotype) method.
Resolves #1286. After commit 525fda8, we don't
set several of the fields in `Variant` when nested in a `Genotype`. Here, we add
code to `ReferenceRegion` to pull the fields that are not set in the nested
`Variant` from the core `Genotype` fields.

fnothaft added a commit to fnothaft/adam that referenced this issue Dec 8, 2016

[ADAM-1286] Fixed ReferenceRegion.apply(genotype: Genotype) method.
Resolves #1286. After commit 525fda8, we don't
set several of the fields in `Variant` when nested in a `Genotype`. Here, we add
code to `ReferenceRegion` to pull the fields that are not set in the nested
`Variant` from the core `Genotype` fields.

@heuermh heuermh closed this in c49191b Dec 8, 2016

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