Package org.broadinstitute.hellbender.engine.spark
package org.broadinstitute.hellbender.engine.spark
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ClassDescriptionA Spark version of
AssemblyRegionWalker.Find assembly regions from reads in a distributed Spark setting.GATKRegistrator registers Serializers for our project.Base class for GATK spark tools that accept standard kinds of inputs (reads, reference, and/or intervals).Encapsulates aSimpleIntervalwith the reads that overlap it (theReadsContextand itsReferenceContextandFeatureContext.A Spark version ofIntervalWalker.A Spark version ofLocusWalker.An extension of Hadoop'sLocalFileSystemthat doesn't write (or verify) .crc files.A Spark version ofReadWalker.Efficient serializer for SAMRecords that uses SAMRecordSparkCodec for encoding/decoding.Efficient serializer for SAMRecordToGATKReadAdapters that uses SAMRecordSparkCodec for encoding/decoding.Command line arguments needed for configuring a spark contextManages creation of the Spark context.Utility methods for shardingLocatableobjects (such as reads) for given intervals, without using a shuffle.Encapsulates aVariantContextwith the reads that overlap it (theReadsContextand itsReferenceContextandFeatureContext.A Spark version ofVariantWalker.