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bigdatagenomics / bdg-formats

Open source formats for scalable genomic processing systems using Avro. Apache 2 licensed.
Apache License 2.0
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[FORMATS-106] Refactor Genotype and GenotypeAnnotation. #176

Closed heuermh closed 3 years ago

heuermh commented 5 years ago

Fixes #106 Incorporates feedback from and replaces #108. Note the diff is somewhat hard to read, for review please consider the whole file link.

AmplabJenkins commented 5 years ago

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/188/ Test PASSed.

AmplabJenkins commented 5 years ago

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/189/ Test PASSed.

heuermh commented 5 years ago

Note in #120 we use VariantAnnotation.readDepth for VCF INFO reserved key AD split to alternate read depth and VariantAnnotation.referenceReadDepth for VCF INFO reserved key AD split to reference read depth. VCF INFO reserved key DP "Combined depth across samples" is not mapped, because it doesn't make any sense after splitting.

This pull request uses GenotypeAnnotation.alternateReadDepth and AnnotationGenotype.referenceReadDepth for VCF FORMAT genotype reserved key AD, and Genotype.readDepth for VCF FORMAT genotype reserved key DP "Read depth". Should this be updated to do the same (i.e. drop DP mapping to readDepth and rename GenotypeAnnotation.alternateReadDepth to GenotypeAnnotation.readDepth)?

AmplabJenkins commented 5 years ago

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/191/ Test PASSed.

AmplabJenkins commented 5 years ago

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/192/ Test PASSed.

AmplabJenkins commented 5 years ago

Test PASSed. Refer to this link for build results (access rights to CI server needed): https://amplab.cs.berkeley.edu/jenkins//job/bdg-formats-prb/200/ Test PASSed.

heuermh commented 3 years ago

Closing as WontFix. Unfortunately there isn't a driver or reviewer for landing this large change.