rdd

Type Members

1. class ADAMContext extends Serializable with Logging

2. class ADAMRDDFunctions[T] extends Serializable

3. abstract class ADAMSequenceDictionaryRDDAggregator[T] extends Serializable with Logging

   A class that provides functions to recover a sequence dictionary from a generic RDD of records.

4. class ADAMSpecificRecordSequenceDictionaryRDDAggregator[T] extends ADAMSequenceDictionaryRDDAggregator[T]

   A class that provides functions to recover a sequence dictionary from a generic RDD of records that are defined in Avro.

5. class AlignmentRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[AlignmentRecord]

6. case class DuplicateMetrics(total: Long, bothMapped: Long, onlyReadMapped: Long, crossChromosome: Long) extends Product with Serializable

7. case class FlagStatMetrics(total: Long, duplicatesPrimary: DuplicateMetrics, duplicatesSecondary: DuplicateMetrics, mapped: Long, pairedInSequencing: Long, read1: Long, read2: Long, properlyPaired: Long, withSelfAndMateMapped: Long, singleton: Long, withMateMappedToDiffChromosome: Long, withMateMappedToDiffChromosomeMapQ5: Long, failedQuality: Boolean) extends Product with Serializable

8. case class Footer(rowGroups: Seq[ParquetRowGroup]) extends Product with Serializable

9. class GenomicRegionPartitioner extends Partitioner with Logging

   GenomicRegionPartitioner partitions ReferencePosition objects into separate, spatially-coherent regions of the genome.

10. case class GenotypesSummary(perSampleStatistics: StatisticsMap, singletonCount: Long, distinctVariantCount: Long) extends Product with Serializable

    Summary statistics for a set of genotypes.

11. case class GenotypesSummaryCounts(genotypesCounts: GenotypeAlleleCounts, singleNucleotideVariantCounts: VariantCounts, multipleNucleotideVariantCount: Long, insertionCount: Long, deletionCount: Long, readCount: Option[Long], phasedCount: Long) extends Product with Serializable

    Simple counts of various properties across a set of genotypes.

12. class MultiContigNonoverlappingRegions extends Serializable

    Creates a multi-reference-region collection of NonoverlappingRegions -- see the scaladocs to NonoverlappingRegions.

13. class NonoverlappingRegions extends Serializable

    The evaluation of a regionJoin takes place with respect to a complete partition on the total space of the genome.

14. class NucleotideContigFragmentRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[NucleotideContigFragment]

15. case class ParquetColumnChunk(numValues: Long, dataPageOffset: Long, indexPageOffset: Option[Long], dictionaryPageOffset: Option[Long], uncompressedSize: Long, compressedSize: Long, columnDescriptor: ParquetColumnDescriptor, compressionCodec: CompressionCodec) extends Product with Serializable

16. case class ParquetColumnDescriptor(path: Seq[String], typeName: PrimitiveTypeName, typeLength: Int, maxRep: Int, maxDef: Int) extends Product with Serializable

17. case class ParquetRowGroup(byteSize: Long, rowCount: Long, columnChunks: Seq[ParquetColumnChunk]) extends Product with Serializable

18. class PileupRDDFunctions extends Serializable with Logging

19. class RodRDDFunctions extends Serializable with Logging