fixes to load properly VCF samples dict from _samples.avro#9
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jpdna wants to merge 4 commits intofnothaft:genotypes-rddfrom
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fixes to load properly VCF samples dict from _samples.avro#9jpdna wants to merge 4 commits intofnothaft:genotypes-rddfrom
jpdna wants to merge 4 commits intofnothaft:genotypes-rddfrom
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Resolves bigdatagenomics#909: * Refactors `org.bdgenomics.adam.rdd.variation` to add `GenomicRDD`s for `Genotype`, `Variant`, and `VariantContext`. These classes write sequence and sample metadata to disk. * Refactors `ADAMRDDFunctions` to an abstract class in preparation for further refactoring in bigdatagenomics#1011. * Added `AvroGenomicRDD` trait which consolidates Parquet + Avro metadata writing code across all Avro data models.
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This PR fixes a problem that in current code the sequence of actions:
ADAMContext.loadGenotypes()fails for two reasons:
_rgdict.avrowhen in fact the vcf derived sample metadata is named_samples.avroThis PR fixes these issues such that writing and loading genotype data works correctly.