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Implement VariantStats OpenCGA Analysis #1376

Open
3 of 4 tasks
j-coll opened this issue Oct 9, 2019 · 0 comments
Open
3 of 4 tasks

Implement VariantStats OpenCGA Analysis #1376

j-coll opened this issue Oct 9, 2019 · 0 comments
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@j-coll
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analysis storage
Milestone
v2.0.0

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@j-coll
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j-coll commented Oct 9, 2019 •
edited

Currently the VariantStats are considered an internal storage operation. We need an Analysis to allow users compute stats over any set of samples, given any input query.

Tasks

  • Implement Analysis
  • Implement default executor using OpenCGA-Storage API
  • Implement HBase MapReduce executor
  • Implement MongoDB Local executor
@j-coll j-coll added this to the v2.0.0 milestone Oct 9, 2019
@j-coll j-coll self-assigned this Oct 9, 2019
j-coll added a commit that referenced this issue Oct 17, 2019
@j-coll
storage: Allow VariantStatsDriver write to file or hbase. #1376
cbec854
j-coll added a commit that referenced this issue Oct 17, 2019
@j-coll
analysis: Implement VariantStats OpenCGA Analysis #1376
ada07e1
j-coll added a commit that referenced this issue Oct 17, 2019
@j-coll
storage: Implement VariantStatsHBaseMapReduceAnalysisExecutor #1376
eb9784a
j-coll added a commit that referenced this issue Oct 17, 2019
@j-coll
analysis: Implement VariantStatsMongoDBLocalAnalysisExecutor. #1376
61df855
j-coll added a commit that referenced this issue Nov 28, 2019
@j-coll
analysis: Fix VariantStatsAnalysis when using a cohort instead of a l…
2451070 
…ist of samples. #1376
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v2.0.0
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