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Accessing GenomicRDD join functions in python #1728

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akmorrow13 opened this issue Sep 15, 2017 · 2 comments
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Accessing GenomicRDD join functions in python #1728

akmorrow13 opened this issue Sep 15, 2017 · 2 comments
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Release 0.24.0
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0.24.0

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@akmorrow13
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@akmorrow13 akmorrow13 commented Sep 15, 2017

I would like to be able to access join functionality in adam-python. Would the best way to do this be to create a wrapper accessing the GenomicRDD joins or do something new with SparkSQL? Any thoughts?
@fnothaft
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@fnothaft fnothaft commented Sep 17, 2017

You'll need both. Specifically, you'll need a wrapper around the region join for python (easy) and you'll need an implementation of GenericGenomicRDD that extends GenomicDataset (hard). Let's chat about this on Monday.
@fnothaft fnothaft added this to the 0.24.0 milestone Dec 6, 2017
@heuermh heuermh added this to Triage in Release 0.24.0 Jan 4, 2018
@heuermh
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@heuermh heuermh commented Jan 9, 2018

@fnothaft push to 0.25.0?
@fnothaft fnothaft mentioned this issue Jan 9, 2018
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fnothaft pushed a commit to fnothaft/adam that referenced this issue Feb 21, 2018
Frank Austin Nothaft
Add functions to support dataset API from generic genomic datasets.
b75295e 
WIP towards bigdatagenomics#1728.
@fnothaft fnothaft mentioned this issue Feb 21, 2018
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fnothaft pushed a commit to fnothaft/adam that referenced this issue Mar 7, 2018
Frank Austin Nothaft
Add functions to support dataset API from generic genomic datasets.
fb561d7 
WIP towards bigdatagenomics#1728.
fnothaft pushed a commit to fnothaft/adam that referenced this issue Mar 7, 2018
Frank Austin Nothaft
[ADAM-1728] Expose region join API through Python.
f915915 
Resolves bigdatagenomics#1728.
fnothaft pushed a commit to fnothaft/adam that referenced this issue Mar 7, 2018
Frank Austin Nothaft
[ADAM-1728] Expose region join API through Python and R.
6184711 
Resolves bigdatagenomics#1728.
fnothaft pushed a commit to fnothaft/adam that referenced this issue Mar 7, 2018
Frank Austin Nothaft
[ADAM-1728] Expose region join API through Python and R.
a26047a 
Resolves bigdatagenomics#1728.
fnothaft pushed a commit to fnothaft/adam that referenced this issue Mar 15, 2018
Frank Austin Nothaft
[ADAM-1728] Expose region join API through Python and R.
40043e5 
Resolves bigdatagenomics#1728.
@heuermh heuermh closed this in a28da44 Mar 20, 2018
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@heuermh @fnothaft @akmorrow13