A class that provides functions to recover a sequence dictionary from a generic RDD of records.
A class that provides functions to recover a sequence dictionary from a generic RDD of records that are defined in Avro.
A base is 'covered' by a region set if any region in the set contains the base itself.
Partition a genome into a set of bins.
GenomicPositionPartitioner partitions ReferencePosition objects into separate, spatially-coherent regions of the genome.
PairingRDD provides some simple helper methods, allowing us take an RDD (presumably an RDD whose values are in some reasonable or intelligible order within and across partitions) and get paired or windowed views on that list of items.
Repartitions objects that are keyed by a ReferencePosition or ReferenceRegion into a single partition per contig.
Contains multiple implementations of a 'region join', an operation that joins two sets of regions based on the spatial overlap between the regions.