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Expose VariantContextRDD in R/Python #1614

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fnothaft opened this Issue Jul 21, 2017 · 0 comments

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fnothaft commented Jul 21, 2017

Realized we are missing this while going through #1613.

@fnothaft fnothaft added this to the 0.23.0 milestone Jul 21, 2017

@fnothaft fnothaft self-assigned this Jul 21, 2017

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 24, 2017

[ADAM-1614] Add VariantContextRDD to R and Python APIs.
Resolves bigdatagenomics#1614. Restructures both R and Python APIs to add `GenomicDataset`
class, which inherits from `GenomicRDD`, as in adam-core. Moves all implementing
classes onto `GenomicDataset`, and adds `VariantContextRDD` which is the lone
class that extends `GenomicRDD`. Deletes `saveAsVcf` from `GenotypeRDD` and
`VariantRDD`, and moves this functionality into `toVariantContextRDD` functions
and `VariantContextRDD.saveAsVcf`. Additionally, adds `sort` and
`sortLexicographically` to the R API, and fixes `sortLexicographically` in
the Python API (it was calling `sort` previously).

fnothaft added a commit to fnothaft/adam that referenced this issue Jul 24, 2017

[ADAM-1614] Add VariantContextRDD to R and Python APIs.
Resolves bigdatagenomics#1614. Restructures both R and Python APIs to add `GenomicDataset`
class, which inherits from `GenomicRDD`, as in adam-core. Moves all implementing
classes onto `GenomicDataset`, and adds `VariantContextRDD` which is the lone
class that extends `GenomicRDD`. Deletes `saveAsVcf` from `GenotypeRDD` and
`VariantRDD`, and moves this functionality into `toVariantContextRDD` functions
and `VariantContextRDD.saveAsVcf`. Additionally, adds `sort` and
`sortLexicographically` to the R API, and fixes `sortLexicographically` in
the Python API (it was calling `sort` previously).

heuermh added a commit that referenced this issue Jul 25, 2017

[ADAM-1614] Add VariantContextRDD to R and Python APIs.
Resolves #1614. Restructures both R and Python APIs to add `GenomicDataset`
class, which inherits from `GenomicRDD`, as in adam-core. Moves all implementing
classes onto `GenomicDataset`, and adds `VariantContextRDD` which is the lone
class that extends `GenomicRDD`. Deletes `saveAsVcf` from `GenotypeRDD` and
`VariantRDD`, and moves this functionality into `toVariantContextRDD` functions
and `VariantContextRDD.saveAsVcf`. Additionally, adds `sort` and
`sortLexicographically` to the R API, and fixes `sortLexicographically` in
the Python API (it was calling `sort` previously).

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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