rdd

Type Members

class ADAMContext extends Serializable with Logging
class ADAMNucleotideContigFragmentRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[ADAMNucleotideContigFragment]
class ADAMPileupRDDFunctions extends Serializable with Logging
class ADAMRDDFunctions[T] extends Serializable
class ADAMRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[ADAMRecord]
class ADAMRodRDDFunctions extends Serializable with Logging
abstract class ADAMSequenceDictionaryRDDAggregator[T] extends Serializable with Logging

A class that provides functions to recover a sequence dictionary from a generic RDD of records.
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.
case class DuplicateMetrics(total: Long, bothMapped: Long, onlyReadMapped: Long, crossChromosome: Long) extends Product with Serializable
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
class GenomicRegionPartitioner extends Partitioner

GenomicRegionPartitioner partitions ReferencePosition objects into separate, spatially-coherent regions of the genome.
case class GenotypesSummary(perSampleStatistics: StatisticsMap, singletonCount: Long, distinctVariantCount: Long) extends Product with Serializable

Summary statistics for a set of genotypes.
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.
class MultiContigNonoverlappingRegions extends Serializable

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

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

Value Members

object ADAMContext extends Serializable
object DuplicateMetrics extends Serializable
object FlagStat
object FlagStatMetrics extends Serializable
object GenomicRegionPartitioner extends Serializable
object GenotypesSummary extends Serializable
object GenotypesSummaryCounts extends Serializable
object GenotypesSummaryFormatting

Functions for converting a GenotypesSummary object to various text formats.
object MultiContigNonoverlappingRegions extends Serializable
object NonoverlappingRegions extends Serializable
object RegionJoin

Contains multiple implementations of a 'region join', an operation that joins two sets of regions based on the spatial overlap between the regions.
package comparisons
package recalibration
package variation

package rdd

Type Members

class ADAMContext extends Serializable with Logging

class ADAMNucleotideContigFragmentRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[ADAMNucleotideContigFragment]

class ADAMPileupRDDFunctions extends Serializable with Logging

class ADAMRDDFunctions[T] extends Serializable

class ADAMRecordRDDFunctions extends ADAMSequenceDictionaryRDDAggregator[ADAMRecord]

class ADAMRodRDDFunctions extends Serializable with Logging

abstract class ADAMSequenceDictionaryRDDAggregator[T] extends Serializable with Logging

class ADAMSpecificRecordSequenceDictionaryRDDAggregator[T] extends ADAMSequenceDictionaryRDDAggregator[T]

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

class GenomicRegionPartitioner extends Partitioner

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

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

class MultiContigNonoverlappingRegions extends Serializable

class NonoverlappingRegions extends Serializable

Value Members

object ADAMContext extends Serializable

object DuplicateMetrics extends Serializable

object FlagStat

object FlagStatMetrics extends Serializable

object GenomicRegionPartitioner extends Serializable

object GenotypesSummary extends Serializable

object GenotypesSummaryCounts extends Serializable

object GenotypesSummaryFormatting

object MultiContigNonoverlappingRegions extends Serializable

object NonoverlappingRegions extends Serializable

object RegionJoin

package comparisons

package recalibration

package variation

Ungrouped