Package org.broadinstitute.hellbender.engine.spark.datasources
package org.broadinstitute.hellbender.engine.spark.datasources
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ClassDescriptionReadsSparkSink writes GATKReads to a file.Loads the reads from disk either serially (using samReaderFactory) or in parallel using Hadoop-BAM.Class to load a reference sequence from a fasta file on Spark.Class to load a reference sequence from a fasta file on HDFS.Wrapper to load a reference sequence from a file stored on HDFS, GCS, or locally.Internal interface to load a reference sequence.A ReferenceSource impl that is backed by a .2bit representation of a reference genome.A library of reference window functions suitable for passing in to transforms such as AddContextDataToRead.A function for requesting a fixed number of extra bases of reference context on either side of each read.VariantsSparkSink writes variants to a VCF file in parallel using Hadoop-BAM.VariantsSparkSource loads Variants from files serially (using FeatureDataSource
) or in parallel using Hadoop-BAM.