adam

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BAM/BED to parquet

3

Hello, Would it be possible to provide a minimal example be it in Scala/python/CLI, how to convert say BAM to an ADAMs parquet? Same with a canonical 6 columns BED....

darked89

heuermh

After removing patches from the bioconda recipe for 0.23.0, the ADAM startup scripts still don't resolve correctly when symlinks ``` + source /opt/conda/bin/activate /opt/conda/conda-bld/adam_1522259566898/_t_env + /bin/bash -x -e /opt/conda/conda-bld/adam_1522259566898/test_tmp/run_test.sh +...

heuermh

Follow on to https://github.com/bigdatagenomics/adam/pull/1837.

fnothaft

After #1921 merges, VariantContextRDD will be usable from Python and R. We should surface: * `loadVcf` * `loadIndexedVcf` * `loadVcfWithProjection` * `loadParquetVariantContexts` in both Python and R.

fnothaft

Pipe API without expectation that return value is GenomicRDD

5

heuermh

Performance issue in TreeRegionJoin

2

Crosslinking to https://github.com/bigdatagenomics/avocado/issues/202. I'm seeing really odd performance issues in Avocado when using the Broadcast region join code. E.g., multiple order of magnitude slowdowns.

fnothaft

Improve Ensembl VEP mapping to TranscriptEffect

1

See https://github.com/bigdatagenomics/bdg-formats/issues/202 https://github.com/heuermh/bdg-formats/blob/docs/docs/source/transcript-effects.md

heuermh

See conversation on Gitter at https://gitter.im/bigdatagenomics/adam?at=5f4343ca59ac794e02c0c60a

heuermh

Refactor Dataset save methods for consistency

2

Abstract classes ```scala trait GenomicDataset[T, U

heuermh