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[ADAM-1996] Load and save VariantContexts as partitioned Parquet. #2001

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merged 2 commits into from
Jun 27, 2018
Merged

[ADAM-1996] Load and save VariantContexts as partitioned Parquet. #2001

merged 2 commits into from
Jun 27, 2018

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heuermh
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@heuermh heuermh commented Jun 21, 2018 •
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Fixes #1996.

heuermh
heuermh commented Jun 21, 2018
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adam-core/src/main/scala/org/bdgenomics/adam/rdd/variant/VariantContextRDD.scala
override val isPartitioned: Boolean = true,
override val optPartitionBinSize: Option[Int] = Some(1000000),
override val optLookbackPartitions: Option[Int] = Some(1)) extends VariantContextRDD
with DatasetBoundGenomicDataset[VariantContext, VariantContextProduct, VariantContextRDD] {
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I'm not fully aware of the implications of adding this trait, thought it preferable to copying the referenceRegionsToDatasetQueryString and filterByOverlappingRegions methods

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This trait should be mixed in, so LGTM.

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Coverage Status

Coverage decreased (-0.1%) to 79.049% when pulling f544f01 on heuermh:partitioned-variant-contexts into f05aa98 on bigdatagenomics:master.

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Coverage Status

Coverage decreased (-0.1%) to 79.049% when pulling f544f01 on heuermh:partitioned-variant-contexts into f05aa98 on bigdatagenomics:master.

@coveralls
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Coverage Status

Coverage decreased (-0.1%) to 79.049% when pulling f544f01 on heuermh:partitioned-variant-contexts into f05aa98 on bigdatagenomics:master.

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coveralls commented Jun 21, 2018 •
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Coverage Status

Coverage increased (+0.2%) to 79.39% when pulling b42e69b on heuermh:partitioned-variant-contexts into f05aa98 on bigdatagenomics:master.

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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2773/
Test PASSed.

@heuermh heuermh requested review from fnothaft and jpdna June 22, 2018 20:25
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Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/2774/
Test PASSed.

@heuermh heuermh added this to the 0.24.1 milestone Jun 23, 2018
@fnothaft fnothaft merged commit 28bcd56 into bigdatagenomics:master Jun 27, 2018
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Merged! Thanks @heuermh!

@heuermh heuermh deleted the partitioned-variant-contexts branch June 28, 2018 21:48
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@fnothaft fnothaft fnothaft approved these changes

@jpdna jpdna Awaiting requested review from jpdna

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