The ADAMContext provides functions on top of a SparkContext for loading genomic data.
Argument configuration for saving any output format.
An abstract class that extends GenomicRDD and where the underlying data is Avro IndexedRecords.
An abstract class describing a GenomicRDD where:
Extends the ShuffleRegionJoin trait to implement a full outer join.
Partition a genome into a set of bins.
GenomicPositionPartitioner partitions ReferencePosition objects into separate, spatially-coherent regions of the genome.
A trait that wraps an RDD of genomic data with helpful metadata.
A partitioner for ReferenceRegion-keyed data.
Formats data going into a pipe to an invoked process.
A trait for singleton objects that build an InFormatter from a GenomicRDD.
Extends the ShuffleRegionJoin trait to implement an inner join.
Extends the ShuffleRegionJoin trait to implement an inner join followed by grouping by the left value.
Implements an inner region join where the left side of the join is broadcast.
Performs an inner region join, followed logically by grouping by the right value.
Extends the ShuffleRegionJoin trait to implement a left outer join.
An abstract class that extends the MultisampleGenomicRDD trait, where the data are Avro IndexedRecords.
A trait describing a GenomicRDD with data from multiple samples.
Deserializes data coming out of a pipe from an invoked process.
Repartitions objects that are keyed by a ReferencePosition or ReferenceRegion into a single partition per contig.
A trait describing a join in the genomic coordinate space between two RDDs where the values are keyed by a ReferenceRegion.
Extends the ShuffleRegionJoin trait to implement a right outer join.
Extends the ShuffleRegionJoin trait to implement a right outer join followed by grouping by all non-null left values.
Implements a right outer region join where the left side of the join is broadcast.
Performs a right outer region join, followed logically by grouping by the right value.
A trait describing join implementations that are based on a sort-merge join.
Implements a shuffle free (broadcast) region join.
A trait for genomic data that is not aligned to a reference (e.
This singleton provides an implicit conversion from a SparkContext to the ADAMContext, as well as implicit functions for the Pipe API.
Helper for creating genomic position partitioners.
Helper object for creating GenomicRegionPartitioners.