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Clarify strandedness in ReferenceRegion apply methods #1285

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fnothaft opened this issue Nov 20, 2016 · 0 comments
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Clarify strandedness in ReferenceRegion apply methods #1285

fnothaft opened this issue Nov 20, 2016 · 0 comments
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@fnothaft fnothaft commented Nov 20, 2016

Given the discussion by me @akmorrow13 and @jpdna in bigdatagenomics/utils#93 (comment), we should probably clarify this. My proposal is:

  • No apply methods for datatypes that can be stranded (AlignmentRecords and Features?)
  • Instead, two methods:
    • def independent which returns a reference region with an independent strand
    • def stranded which returns a reference region with orientation set

We'd then want to modify something in GenomicRDD to clarify whether the data in the RDD is stranded or not, for data that can be strand (in)dependent.

I'll take a quick hack at this tomorrow; should be a quick change. If everyone thinks it looks good, we can get it in 0.21.0, else we can push it.

@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
… methods.

Resolves bigdatagenomics#1285. Removes `ReferenceRegion.apply` methods for `Feature` and
`AlignmentRecord` schemas, and replaces with `stranded` and `unstranded`.
fnothaft added a commit to fnothaft/adam that referenced this issue Dec 8, 2016
… methods.

Resolves bigdatagenomics#1285. Removes `ReferenceRegion.apply` methods for `Feature` and
`AlignmentRecord` schemas, and replaces with `stranded` and `unstranded`.
fnothaft added a commit to fnothaft/adam that referenced this issue Dec 8, 2016
… 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.
@heuermh heuermh closed this in #1291 Dec 8, 2016
heuermh added a commit that referenced this issue Dec 8, 2016
… methods.

Resolves #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.
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