Uses of Package
com.intel.genomicsdb

Classes in com.intel.genomicsdb used by com.intel.genomicsdb

Class and Description
ChromosomeInterval Utility class to represent a chromosome interval Contains 3 members - chr name, start, end (1-based)
GenomicsDBCallsetsMapProto.CallsetMappingPB Protobuf type CallsetMappingPB
GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder Protobuf type CallsetMappingPB
GenomicsDBCallsetsMapProto.CallsetMappingPBOrBuilder
GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap Protobuf type SampleIDToTileDBIDMap
GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder Protobuf type SampleIDToTileDBIDMap
GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder
GenomicsDBConfiguration The configuration class enables users to use Java/Scala to populate the input parameters of GenomicsDB.
GenomicsDBException Classes in the genomicsdb package throw exceptions of type GenomicsDBException
GenomicsDBExportConfiguration.ColumnRange Protobuf type ColumnRange
GenomicsDBExportConfiguration.ColumnRange.Builder Protobuf type ColumnRange
GenomicsDBExportConfiguration.ColumnRangeList Protobuf type ColumnRangeList
GenomicsDBExportConfiguration.ColumnRangeList.Builder Protobuf type ColumnRangeList
GenomicsDBExportConfiguration.ColumnRangeListOrBuilder
GenomicsDBExportConfiguration.ColumnRangeOrBuilder
GenomicsDBExportConfiguration.ExportConfiguration Protobuf type ExportConfiguration
GenomicsDBExportConfiguration.ExportConfiguration.Builder Protobuf type ExportConfiguration
GenomicsDBExportConfiguration.ExportConfigurationOrBuilder
GenomicsDBFeatureReader A reader for GenomicsDB that implements FeatureReader Currently, the reader only return VariantContext
GenomicsDBFeatureReader.GenomicsDBFeatureIterator Iterator over VariantContext objects.
GenomicsDBImportConfiguration.ImportConfiguration Protobuf type ImportConfiguration
GenomicsDBImportConfiguration.ImportConfiguration.Builder Protobuf type ImportConfiguration
GenomicsDBImportConfiguration.ImportConfigurationOrBuilder
GenomicsDBImportConfiguration.Partition Protobuf type Partition
GenomicsDBImportConfiguration.Partition.Builder Protobuf type Partition
GenomicsDBImportConfiguration.PartitionOrBuilder
GenomicsDBImporterStreamWrapper Utility class wrapping a stream and a VariantContextWriter for a given stream Each GenomicsDB import stream consists of a buffer stream and a writer object If the caller provides an iterator, then mCurrentVC points to the VariantContext object to be written, if any.
GenomicsDBInputFormat
GenomicsDBPartitionInfo Maintain global information on how variant data is partitioned across multiple nodes (if loaded with mpiexec) The assumption is that every object described one partition as: {"begin": 0, "workspace":"/home/forall/tiledb-ws", "array": "test0", "vcf_output_filename":"/home/forall/lihao/mytest/test0.vcf.gz" }
GenomicsDBQueryStream Provides a java.io.InputStream interface for the GenomicsDB combine gVCF operation.
GenomicsDBTimer
GenomicsDBVidMapProto.Chromosome Protobuf type Chromosome
GenomicsDBVidMapProto.Chromosome.Builder Protobuf type Chromosome
GenomicsDBVidMapProto.ChromosomeOrBuilder
GenomicsDBVidMapProto.InfoField Protobuf type InfoField
GenomicsDBVidMapProto.InfoField.Builder Protobuf type InfoField
GenomicsDBVidMapProto.InfoFieldOrBuilder
GenomicsDBVidMapProto.VidMappingPB Protobuf type VidMappingPB
GenomicsDBVidMapProto.VidMappingPB.Builder Protobuf type VidMappingPB
GenomicsDBVidMapProto.VidMappingPBOrBuilder
MultiChromosomeIterator Given an AbstractFeatureReader over VariantContext objects and a list of ChromosomeInterval objects, this class is an Iterator over VariantContext for all the chromosome intervals in the list
SampleInfo Utility class that stores row index and globally unique name for a given sample
SilentByteBufferStream Buffer stream implementation - it's silent in the sense that when the buffer is full, it doesn't raise an exception but just marks a a flag as full.