Reference region cleanup #1291
Reference region cleanup #1291
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Test PASSed. |
| new ReferenceRegion(feature.getContigName, feature.getStart, feature.getEnd) | ||
| } | ||
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| /** | ||
| * Builds a reference region for a feature without strand information. |
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without strand information. → with strand set.
| def stranded(feature: Feature): ReferenceRegion = { | ||
| checkFeature(feature) | ||
| require(feature.getStrand != null, | ||
| "Strand is not defined in feature %s.".format(feature)) |
| @@ -148,7 +148,9 @@ object ReferenceRegion { | |||
| * @return The site where this genotype lives. | |||
| */ | |||
| def apply(genotype: Genotype): ReferenceRegion = { | |||
| ReferenceRegion(genotype.getVariant) | |||
| ReferenceRegion(genotype.getContigName, | |||
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A few general questions (not about this line specifically):
Rename ReferenceRegion.orientation to ReferenceRegion.strand?
Add strand parameters to other methods (e.g. fromStart, toEnd, all)?
Set strand when copying from one ReferenceRegion to another (i.e. line 234)?
Resolves bigdatagenomics#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
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Thanks for the comments @heuermh. I've rebased and pushed two commits addressing your comments. When this looks good to you, I'll squash commits 2–4 down into a single commit for merge. |
… methods. Resolves bigdatagenomics#1285. Removes `ReferenceRegion.apply` methods for `Feature` and `AlignmentRecord` schemas, and replaces with `stranded` and `unstranded`. Additionally, we change `orientation` to `strand` thoughout Reference{Region, Position} and add strand as an optional argument on the various apply-like methods.
fnothaft
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Squashed down. |
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Test PASSed. |
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Thank you, @fnothaft |
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Test PASSed. |
Resolves #1285 and #1286. The first two commits need to be squashed together.