Index (com.intel:genomicsdb-gatk4 0.4.0 API)

A B C D E F G H I J L M N O P Q R S T U V W

A

add(VariantContext, int) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Write VariantContext object to stream - may fail if the buffer is full It's the caller's responsibility keep track of the VC object that's not written
addAllAttributes(Iterable<String>) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
addAllChromosomes(Iterable<? extends GenomicsDBVidMapProto.Chromosome>) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
addAllColumnPartitions(Iterable<? extends GenomicsDBImportConfiguration.Partition>) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
addAllInfofields(Iterable<? extends GenomicsDBVidMapProto.InfoField>) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
addAllQueryColumnRanges(Iterable<? extends GenomicsDBExportConfiguration.ColumnRangeList>) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
addAllRangeList(Iterable<? extends GenomicsDBExportConfiguration.ColumnRange>) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
addAllVcfFieldClass(Iterable<String>) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
addAttributes(String) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
addAttributesBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
addBufferStream(String, VCFHeader, long, VariantContextWriterBuilder.OutputType, Map<Integer, SampleInfo>) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Add a buffer stream as the data source - caller must: 1.
addBufferStream(String, VCFHeader, long, VariantContextWriterBuilder.OutputType, Iterator<VariantContext>, Map<Integer, SampleInfo>) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Add a buffer stream or VC iterator - internal function
addChromosomes(GenomicsDBVidMapProto.Chromosome) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
addChromosomes(int, GenomicsDBVidMapProto.Chromosome) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
addChromosomes(GenomicsDBVidMapProto.Chromosome.Builder) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
addChromosomes(int, GenomicsDBVidMapProto.Chromosome.Builder) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
addChromosomesBuilder() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
addChromosomesBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
addColumnPartitions(GenomicsDBImportConfiguration.Partition) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
addColumnPartitions(int, GenomicsDBImportConfiguration.Partition) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
addColumnPartitions(GenomicsDBImportConfiguration.Partition.Builder) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
addColumnPartitions(int, GenomicsDBImportConfiguration.Partition.Builder) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
addColumnPartitionsBuilder() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
addColumnPartitionsBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
addInfofields(GenomicsDBVidMapProto.InfoField) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
addInfofields(int, GenomicsDBVidMapProto.InfoField) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
addInfofields(GenomicsDBVidMapProto.InfoField.Builder) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
addInfofields(int, GenomicsDBVidMapProto.InfoField.Builder) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
addInfofieldsBuilder() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
addInfofieldsBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
addPartitions(GenomicsDBPartitionInfo) - Method in class com.intel.genomicsdb.GenomicsDBConfiguration
addQueryColumnRanges(GenomicsDBExportConfiguration.ColumnRangeList) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
addQueryColumnRanges(int, GenomicsDBExportConfiguration.ColumnRangeList) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
addQueryColumnRanges(GenomicsDBExportConfiguration.ColumnRangeList.Builder) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
addQueryColumnRanges(int, GenomicsDBExportConfiguration.ColumnRangeList.Builder) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
addQueryColumnRangesBuilder() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
addQueryColumnRangesBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
addRangeList(GenomicsDBExportConfiguration.ColumnRange) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
addRangeList(int, GenomicsDBExportConfiguration.ColumnRange) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
addRangeList(GenomicsDBExportConfiguration.ColumnRange.Builder) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
addRangeList(int, GenomicsDBExportConfiguration.ColumnRange.Builder) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
addRangeListBuilder() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
addRangeListBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
addSortedVariantContextIterator(String, VCFHeader, Iterator<VariantContext>, long, VariantContextWriterBuilder.OutputType, Map<Integer, SampleInfo>) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Add a sorted VC iterator as the data source - caller must: 1.
addVcfFieldClass(String) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
addVcfFieldClassBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
array_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
array_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
ARRAY_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
attributes_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
attributes_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
ATTRIBUTES_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
available() - Method in class com.intel.genomicsdb.GenomicsDBQueryStream

B

begin_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
begin_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
BEGIN_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
beginPosition - Variable in class com.intel.genomicsdb.GenomicsDBPartitionInfo
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
bitField0_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
build() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
Builder() - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
Builder(GeneratedMessage.BuilderParent) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
buildPartial() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder

C

CALLSET_MAP_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
CALLSET_MAPPING_FILE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
callsetMap_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
callsetMap_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
CallsetMapDefaultEntryHolder() - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.CallsetMapDefaultEntryHolder
callsetMappingFile_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
callsetMappingFile_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
CallsetMappingPB(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
CallsetMappingPB() - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
CallsetMappingPB(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
Chromosome(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
Chromosome() - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
Chromosome(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
ChromosomeInterval - Class in com.intel.genomicsdb: Utility class to represent a chromosome interval Contains 3 members - chr name, start, end (1-based)
ChromosomeInterval(String, long, long) - Constructor for class com.intel.genomicsdb.ChromosomeInterval
chromosomes_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
chromosomes_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
CHROMOSOMES_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
chromosomesBuilder_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
clear() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
clearArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string array = 3;
clearAttributes() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
clearBegin() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: required int64 begin = 1;
clearCallsetMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string callset_mapping_file = 6;
clearChromosomes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
clearColumnPartitions() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
clearCompressTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool compress_tiledb_array = 15 [default = true];
clearDeleteAndCreateTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool delete_and_create_tiledb_array = 10 [default = false];
clearDiscardVcfIndex() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool discard_vcf_index = 13 [default = true];
clearDoPingPongBuffering() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool do_ping_pong_buffering = 11 [default = true];
clearEnd() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional int64 end = 5 [default = 9223372036854775807];
clearHigh() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 high = 2;
clearIdxInFile() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int32 idx_in_file = 3;
clearInfofields() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
clearLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 length = 2;
clearLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: optional string length = 4;
clearLow() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 low = 1;
clearName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required string name = 1;
clearName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string name = 1;
clearNumCellsPerTile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 num_cells_per_tile = 16 [default = 1000];
clearNumParallelVcfFiles() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int32 num_parallel_vcf_files = 9 [default = 1];
clearOffloadVcfOutputProcessing() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool offload_vcf_output_processing = 12 [default = true];
clearProduceCombinedVcf() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_combined_vcf = 2 [default = false];
clearProduceTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_tiledb_array = 3 [default = true];
clearQueryColumnRanges() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
clearRangeList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
clearReferenceGenome() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string reference_genome = 3;
clearRowBasedPartitioning() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool row_based_partitioning = 1 [default = false];
clearSampleName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required string sample_name = 1;
clearSegmentSize() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 segment_size = 14 [default = 10485760];
clearSizePerColumnPartition() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: required int64 size_per_column_partition = 7 [default = 10240];
clearStreamName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: optional string stream_name = 4;
clearTiledbArrayName() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_array_name = 2;
clearTiledbColumnOffset() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 tiledb_column_offset = 3;
clearTiledbRowIndex() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int64 tiledb_row_index = 2;
clearTiledbWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_workspace = 1;
clearTreatDeletionsAsIntervals() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool treat_deletions_as_intervals = 8 [default = true];
clearType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string type = 2;
clearVcfFieldClass() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
clearVcfOutputFilename() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string vcf_output_filename = 4;
clearVidMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string vid_mapping_file = 5;
clearWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string workspace = 2;
close() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader
close() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
close() - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
close() - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
close() - Method in class com.intel.genomicsdb.SilentByteBufferStream
COLUMN_PARTITIONS_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
columnPartitionIterator(AbstractFeatureReader<VariantContext, SOURCE>, String, int) - Static method in class com.intel.genomicsdb.GenomicsDBImporter: Utility function that returns a MultiChromosomeIterator given an AbstractFeatureReader that will iterate over the VariantContext objects provided by the reader belonging to the column partition specified by the loader JSON file and rank/partition index
columnPartitionIterator(AbstractFeatureReader<VariantContext, SOURCE>) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Utility function that returns a MultiChromosomeIterator given an AbstractFeatureReader that will iterate over the VariantContext objects provided by the reader belonging to the column partition specified by this object's loader JSON file and rank/partition index
columnPartitions_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
columnPartitions_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
columnPartitionsBuilder_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
ColumnRange(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
ColumnRange() - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
ColumnRange(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
ColumnRangeList(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
ColumnRangeList() - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
ColumnRangeList(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
com.intel.genomicsdb - package com.intel.genomicsdb
COMPRESS_TILEDB_ARRAY_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
compressTiledbArray_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
compressTiledbArray_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
configuration - Variable in class com.intel.genomicsdb.GenomicsDBInputFormat
createImportConfiguration(String, String, Long, Long) - Method in class com.intel.genomicsdb.GenomicsDBImporter
createRecordReader(InputSplit, TaskAttemptContext) - Method in class com.intel.genomicsdb.GenomicsDBInputFormat
currentKey - Variable in class com.intel.genomicsdb.GenomicsDBRecordReader
currentVariant - Variable in class com.intel.genomicsdb.GenomicsDBRecordReader

D

DEFAULT_ARRAYNAME - Variable in class com.intel.genomicsdb.GenomicsDBImporter
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
DEFAULT_INSTANCE - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
DEFAULT_SIZE_PER_COLUMN_PARTITION - Variable in class com.intel.genomicsdb.GenomicsDBImporter
DEFAULT_TILEDB_CELLS_PER_TILE - Variable in class com.intel.genomicsdb.GenomicsDBImporter
defaultEntry - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.CallsetMapDefaultEntryHolder
DELETE_AND_CREATE_TILEDB_ARRAY_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
deleteAndCreateTiledbArray_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
deleteAndCreateTiledbArray_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration
descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration
descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto
DISCARD_VCF_INDEX_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
discardVcfIndex_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
discardVcfIndex_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
DO_PING_PONG_BUFFERING_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
doPingPongBuffering_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
doPingPongBuffering_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration

E

end_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
end_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
END_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
ensureAttributesIsMutable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
ensureChromosomesIsMutable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
ensureColumnPartitionsIsMutable() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
ensureInfofieldsIsMutable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
ensureQueryColumnRangesIsMutable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
ensureRangeListIsMutable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
ensureVcfFieldClassIsMutable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
ExportConfiguration(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
ExportConfiguration() - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
ExportConfiguration(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration

F

featureReader - Variable in class com.intel.genomicsdb.GenomicsDBRecordReader
flush() - Method in class com.intel.genomicsdb.SilentByteBufferStream

G

generateSortedCallSetMap(Map<String, FeatureReader<VariantContext>>, boolean) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Creates a sorted list of callsets and generates unique TileDB row indices for them.
generateVidMapFromMergedHeader(Set<VCFHeaderLine>) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Generate the ProtoBuf data structure for vid mapping Also remember, contigs are 1-based which means TileDB column offsets should start from 1
GenomicsDBCallsetsMapProto - Class in com.intel.genomicsdb
GenomicsDBCallsetsMapProto() - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
GenomicsDBCallsetsMapProto.CallsetMappingPB - Class in com.intel.genomicsdb: Protobuf type CallsetMappingPB
GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder - Class in com.intel.genomicsdb: Protobuf type CallsetMappingPB
GenomicsDBCallsetsMapProto.CallsetMappingPB.CallsetMapDefaultEntryHolder - Class in com.intel.genomicsdb
GenomicsDBCallsetsMapProto.CallsetMappingPBOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap - Class in com.intel.genomicsdb: Protobuf type SampleIDToTileDBIDMap
GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder - Class in com.intel.genomicsdb: Protobuf type SampleIDToTileDBIDMap
GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBConfiguration - Class in com.intel.genomicsdb: The configuration class enables users to use Java/Scala to populate the input parameters of GenomicsDB.
GenomicsDBConfiguration(Configuration) - Constructor for class com.intel.genomicsdb.GenomicsDBConfiguration
GenomicsDBConfiguration(Configuration, List<GenomicsDBPartitionInfo>) - Constructor for class com.intel.genomicsdb.GenomicsDBConfiguration: Constructor with partition information
genomicsDBConfiguration - Variable in class com.intel.genomicsdb.GenomicsDBInputFormat
GenomicsDBException - Exception in com.intel.genomicsdb: Classes in the genomicsdb package throw exceptions of type GenomicsDBException
GenomicsDBException(String) - Constructor for exception com.intel.genomicsdb.GenomicsDBException
GenomicsDBException(String, Throwable) - Constructor for exception com.intel.genomicsdb.GenomicsDBException
GenomicsDBExportConfiguration - Class in com.intel.genomicsdb
GenomicsDBExportConfiguration() - Constructor for class com.intel.genomicsdb.GenomicsDBExportConfiguration
GenomicsDBExportConfiguration.ColumnRange - Class in com.intel.genomicsdb: Protobuf type ColumnRange
GenomicsDBExportConfiguration.ColumnRange.Builder - Class in com.intel.genomicsdb: Protobuf type ColumnRange
GenomicsDBExportConfiguration.ColumnRangeList - Class in com.intel.genomicsdb: Protobuf type ColumnRangeList
GenomicsDBExportConfiguration.ColumnRangeList.Builder - Class in com.intel.genomicsdb: Protobuf type ColumnRangeList
GenomicsDBExportConfiguration.ColumnRangeListOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBExportConfiguration.ColumnRangeOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBExportConfiguration.ExportConfiguration - Class in com.intel.genomicsdb: Protobuf type ExportConfiguration
GenomicsDBExportConfiguration.ExportConfiguration.Builder - Class in com.intel.genomicsdb: Protobuf type ExportConfiguration
GenomicsDBExportConfiguration.ExportConfigurationOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBFeatureIterator(String, String, FeatureCodec<T, SOURCE>) - Constructor for class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator: Constructor
GenomicsDBFeatureIterator(String, String, FeatureCodec<T, SOURCE>, String, int, int) - Constructor for class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator: Constructor
GenomicsDBFeatureReader<T extends htsjdk.tribble.Feature,SOURCE> - Class in com.intel.genomicsdb: A reader for GenomicsDB that implements FeatureReader Currently, the reader only return VariantContext
GenomicsDBFeatureReader(String, String, String, String, FeatureCodec<T, SOURCE>) - Constructor for class com.intel.genomicsdb.GenomicsDBFeatureReader: Constructor
GenomicsDBFeatureReader(String, String, String, String, String, FeatureCodec<T, SOURCE>) - Constructor for class com.intel.genomicsdb.GenomicsDBFeatureReader: Constructor
GenomicsDBFeatureReader(String, String, FeatureCodec<T, SOURCE>) - Constructor for class com.intel.genomicsdb.GenomicsDBFeatureReader: Constructor
GenomicsDBFeatureReader(String, FeatureCodec<T, SOURCE>) - Constructor for class com.intel.genomicsdb.GenomicsDBFeatureReader: Constructor
GenomicsDBFeatureReader.GenomicsDBFeatureIterator - Class in com.intel.genomicsdb: Iterator over VariantContext objects.
GenomicsDBImportConfiguration - Class in com.intel.genomicsdb
GenomicsDBImportConfiguration() - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration
GenomicsDBImportConfiguration.ImportConfiguration - Class in com.intel.genomicsdb: Protobuf type ImportConfiguration
GenomicsDBImportConfiguration.ImportConfiguration.Builder - Class in com.intel.genomicsdb: Protobuf type ImportConfiguration
GenomicsDBImportConfiguration.ImportConfigurationOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBImportConfiguration.Partition - Class in com.intel.genomicsdb: Protobuf type Partition
GenomicsDBImportConfiguration.Partition.Builder - Class in com.intel.genomicsdb: Protobuf type Partition
GenomicsDBImportConfiguration.PartitionOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBImporter - Class in com.intel.genomicsdb: Java wrapper for vcf2tiledb - imports VCFs into TileDB/GenomicsDB.
GenomicsDBImporter() - Constructor for class com.intel.genomicsdb.GenomicsDBImporter: Default Constructor
GenomicsDBImporter(String) - Constructor for class com.intel.genomicsdb.GenomicsDBImporter: Constructor
GenomicsDBImporter(String, int) - Constructor for class com.intel.genomicsdb.GenomicsDBImporter: Constructor
GenomicsDBImporter(String, int, long, long) - Constructor for class com.intel.genomicsdb.GenomicsDBImporter: Constructor
GenomicsDBImporter(Map<String, FeatureReader<VariantContext>>, Set<VCFHeaderLine>, ChromosomeInterval, String, String, Long, Long) - Constructor for class com.intel.genomicsdb.GenomicsDBImporter: Constructor to create required data structures from a list of GVCF files and a chromosome interval.
GenomicsDBImporter(Map<String, FeatureReader<VariantContext>>, Set<VCFHeaderLine>, ChromosomeInterval, String, String, Long, Long, boolean) - Constructor for class com.intel.genomicsdb.GenomicsDBImporter: Constructor to create required data structures from a list of GVCF files and a chromosome interval.
GenomicsDBImporter(Map<String, FeatureReader<VariantContext>>, Set<VCFHeaderLine>, ChromosomeInterval, String, String, Long, Long, String) - Constructor for class com.intel.genomicsdb.GenomicsDBImporter: Constructor to create required data structures from a list of GVCF files and a chromosome interval.
GenomicsDBImporterStreamWrapper - Class in com.intel.genomicsdb: 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.
GenomicsDBImporterStreamWrapper(VCFHeader, long, VariantContextWriterBuilder.OutputType, Iterator<VariantContext>) - Constructor for class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper: Constructor
GenomicsDBInputFormat<VCONTEXT extends htsjdk.tribble.Feature,SOURCE> - Class in com.intel.genomicsdb
GenomicsDBInputFormat() - Constructor for class com.intel.genomicsdb.GenomicsDBInputFormat: default constructor
GenomicsDBInputFormat(GenomicsDBConfiguration) - Constructor for class com.intel.genomicsdb.GenomicsDBInputFormat
GenomicsDBInputSplit - Class in com.intel.genomicsdb
GenomicsDBInputSplit() - Constructor for class com.intel.genomicsdb.GenomicsDBInputSplit: Default constructor
GenomicsDBInputSplit(long) - Constructor for class com.intel.genomicsdb.GenomicsDBInputSplit
GenomicsDBJavaSparkFactory - Class in com.intel.genomicsdb: This factory class exposes the two ways JavaRDD of variant contexts (htsjdk) can be retrieved from GenomicsDB.
GenomicsDBJavaSparkFactory() - Constructor for class com.intel.genomicsdb.GenomicsDBJavaSparkFactory
GenomicsDBPartitionInfo - Class in com.intel.genomicsdb: 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" }
GenomicsDBPartitionInfo(Integer, String, String, String) - Constructor for class com.intel.genomicsdb.GenomicsDBPartitionInfo
GenomicsDBQueryStream - Class in com.intel.genomicsdb: Provides a java.io.InputStream interface for the GenomicsDB combine gVCF operation.
GenomicsDBQueryStream(String, String) - Constructor for class com.intel.genomicsdb.GenomicsDBQueryStream: Constructor
GenomicsDBQueryStream(String, String, String, int, int) - Constructor for class com.intel.genomicsdb.GenomicsDBQueryStream: Constructor
GenomicsDBQueryStream(String, String, String, int, int, int) - Constructor for class com.intel.genomicsdb.GenomicsDBQueryStream: Constructor
GenomicsDBQueryStream(String, String, String, int, int, int, long, long) - Constructor for class com.intel.genomicsdb.GenomicsDBQueryStream: Constructor
GenomicsDBRecordReader<VCONTEXT extends htsjdk.tribble.Feature,SOURCE> - Class in com.intel.genomicsdb
GenomicsDBRecordReader(GenomicsDBFeatureReader<VCONTEXT, SOURCE>) - Constructor for class com.intel.genomicsdb.GenomicsDBRecordReader
GenomicsDBTimer - Class in com.intel.genomicsdb
GenomicsDBTimer() - Constructor for class com.intel.genomicsdb.GenomicsDBTimer
GenomicsDBUtils - Class in com.intel.genomicsdb: Utility Java functions for GenomicsDB
GenomicsDBUtils() - Constructor for class com.intel.genomicsdb.GenomicsDBUtils
GenomicsDBVidMapProto - Class in com.intel.genomicsdb
GenomicsDBVidMapProto() - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto
GenomicsDBVidMapProto.Chromosome - Class in com.intel.genomicsdb: Protobuf type Chromosome
GenomicsDBVidMapProto.Chromosome.Builder - Class in com.intel.genomicsdb: Protobuf type Chromosome
GenomicsDBVidMapProto.ChromosomeOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBVidMapProto.InfoField - Class in com.intel.genomicsdb: Protobuf type InfoField
GenomicsDBVidMapProto.InfoField.Builder - Class in com.intel.genomicsdb: Protobuf type InfoField
GenomicsDBVidMapProto.InfoFieldOrBuilder - Interface in com.intel.genomicsdb
GenomicsDBVidMapProto.VidMappingPB - Class in com.intel.genomicsdb: Protobuf type VidMappingPB
GenomicsDBVidMapProto.VidMappingPB.Builder - Class in com.intel.genomicsdb: Protobuf type VidMappingPB
GenomicsDBVidMapProto.VidMappingPBOrBuilder - Interface in com.intel.genomicsdb
getArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string array = 3;
getArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string array = 3;
getArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string array = 3;
getArrayBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string array = 3;
getArrayBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string array = 3;
getArrayBytes() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string array = 3;
getAttributes(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
getAttributes(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated string attributes = 5;
getAttributes(int) - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated string attributes = 5;
getAttributesBytes(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
getAttributesBytes(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated string attributes = 5;
getAttributesBytes(int) - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated string attributes = 5;
getAttributesCount() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
getAttributesCount() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated string attributes = 5;
getAttributesCount() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated string attributes = 5;
getAttributesList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
getAttributesList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated string attributes = 5;
getAttributesList() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated string attributes = 5;
getBegin() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: required int64 begin = 1;
getBegin() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: required int64 begin = 1;
getBegin() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: required int64 begin = 1;
getBuffer() - Method in class com.intel.genomicsdb.SilentByteBufferStream: Get byte buffer for this stream
getCallsetMap() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder: map<string, .SampleIDToTileDBIDMap> callset_map = 1;
getCallsetMap() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB: map<string, .SampleIDToTileDBIDMap> callset_map = 1;
getCallsetMap() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPBOrBuilder: map<string, .SampleIDToTileDBIDMap> callset_map = 1;
getCallsetMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string callset_mapping_file = 6;
getCallsetMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional string callset_mapping_file = 6;
getCallsetMappingFile() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional string callset_mapping_file = 6;
getCallsetMappingFileBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string callset_mapping_file = 6;
getCallsetMappingFileBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional string callset_mapping_file = 6;
getCallsetMappingFileBytes() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional string callset_mapping_file = 6;
getChromosomeIntervalsForColumnPartition(String, int) - Static method in class com.intel.genomicsdb.GenomicsDBImporter: Utility function that returns a list of ChromosomeInterval objects for the column partition specified by the loader JSON file and rank/partition index
getChromosomes(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
getChromosomes(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .Chromosome chromosomes = 2;
getChromosomes(int) - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .Chromosome chromosomes = 2;
getChromosomesBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
getChromosomesBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
getChromosomesCount() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
getChromosomesCount() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .Chromosome chromosomes = 2;
getChromosomesCount() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .Chromosome chromosomes = 2;
getChromosomesFieldBuilder() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
getChromosomesList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
getChromosomesList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .Chromosome chromosomes = 2;
getChromosomesList() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .Chromosome chromosomes = 2;
getChromosomesOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
getChromosomesOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .Chromosome chromosomes = 2;
getChromosomesOrBuilder(int) - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .Chromosome chromosomes = 2;
getChromosomesOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
getChromosomesOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .Chromosome chromosomes = 2;
getChromosomesOrBuilderList() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .Chromosome chromosomes = 2;
getColumnPartitions(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
getColumnPartitions(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: repeated .Partition column_partitions = 4;
getColumnPartitions(int) - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: repeated .Partition column_partitions = 4;
getColumnPartitionsBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
getColumnPartitionsBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
getColumnPartitionsCount() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
getColumnPartitionsCount() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: repeated .Partition column_partitions = 4;
getColumnPartitionsCount() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: repeated .Partition column_partitions = 4;
getColumnPartitionsFieldBuilder() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
getColumnPartitionsList() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
getColumnPartitionsList() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: repeated .Partition column_partitions = 4;
getColumnPartitionsList() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: repeated .Partition column_partitions = 4;
getColumnPartitionsOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
getColumnPartitionsOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: repeated .Partition column_partitions = 4;
getColumnPartitionsOrBuilder(int) - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: repeated .Partition column_partitions = 4;
getColumnPartitionsOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
getColumnPartitionsOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: repeated .Partition column_partitions = 4;
getColumnPartitionsOrBuilderList() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: repeated .Partition column_partitions = 4;
getCompressTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool compress_tiledb_array = 15 [default = true];
getCompressTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool compress_tiledb_array = 15 [default = true];
getCompressTiledbArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool compress_tiledb_array = 15 [default = true];
getConf() - Method in class com.intel.genomicsdb.GenomicsDBInputFormat
getCurrentKey() - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
getCurrentValue() - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
getCurrentVC() - Method in class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper: Returns mCurrentVC - could be null if mIterator is null or !mIterator.hasNext()
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
getDefaultInstance() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
getDefaultInstanceForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
getDeleteAndCreateTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool delete_and_create_tiledb_array = 10 [default = false];
getDeleteAndCreateTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool delete_and_create_tiledb_array = 10 [default = false];
getDeleteAndCreateTiledbArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool delete_and_create_tiledb_array = 10 [default = false];
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
getDescriptor() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
getDescriptorForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
getDiscardVcfIndex() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool discard_vcf_index = 13 [default = true];
getDiscardVcfIndex() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool discard_vcf_index = 13 [default = true];
getDiscardVcfIndex() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool discard_vcf_index = 13 [default = true];
getDoPingPongBuffering() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool do_ping_pong_buffering = 11 [default = true];
getDoPingPongBuffering() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool do_ping_pong_buffering = 11 [default = true];
getDoPingPongBuffering() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool do_ping_pong_buffering = 11 [default = true];
getEnd() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional int64 end = 5 [default = 9223372036854775807];
getEnd() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional int64 end = 5 [default = 9223372036854775807];
getEnd() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional int64 end = 5 [default = 9223372036854775807];
getExhaustedBufferStreamIndex(long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Get buffer stream index of i-th exhausted stream There are mNumExhaustedBufferStreams and the caller must provide data for streams with indexes getExhaustedBufferStreamIndex(0), getExhaustedBufferStreamIndex(1),..., getExhaustedBufferStreamIndex(mNumExhaustedBufferStreams-1)
getHeader() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader: Return the VCF header of the combined gVCF stream
getHigh() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 high = 2;
getHigh() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange: required int64 high = 2;
getHigh() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeOrBuilder: required int64 high = 2;
getHosts() - Method in class com.intel.genomicsdb.GenomicsDBConfiguration
getIdxInFile() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int32 idx_in_file = 3;
getIdxInFile() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: required int32 idx_in_file = 3;
getIdxInFile() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: required int32 idx_in_file = 3;
getInfofields(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
getInfofields(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .InfoField infofields = 1;
getInfofields(int) - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .InfoField infofields = 1;
getInfofieldsBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
getInfofieldsBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
getInfofieldsCount() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
getInfofieldsCount() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .InfoField infofields = 1;
getInfofieldsCount() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .InfoField infofields = 1;
getInfofieldsFieldBuilder() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
getInfofieldsList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
getInfofieldsList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .InfoField infofields = 1;
getInfofieldsList() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .InfoField infofields = 1;
getInfofieldsOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
getInfofieldsOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .InfoField infofields = 1;
getInfofieldsOrBuilder(int) - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .InfoField infofields = 1;
getInfofieldsOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
getInfofieldsOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: repeated .InfoField infofields = 1;
getInfofieldsOrBuilderList() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPBOrBuilder: repeated .InfoField infofields = 1;
getLength(VCFHeaderLine) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Maps the "Number" from INFO or FORMAT fields in VCF header to GenomicsDB lengths.
getLength() - Method in class com.intel.genomicsdb.GenomicsDBInputSplit
getLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 length = 2;
getLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: required int64 length = 2;
getLength() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.ChromosomeOrBuilder: required int64 length = 2;
getLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: optional string length = 4;
getLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: optional string length = 4;
getLength() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: optional string length = 4;
getLengthBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: optional string length = 4;
getLengthBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: optional string length = 4;
getLengthBytes() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: optional string length = 4;
getLocations() - Method in class com.intel.genomicsdb.GenomicsDBInputSplit: Called from NewHadoopRDD.getPreferredLocations(Partition)
getLow() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 low = 1;
getLow() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange: required int64 low = 1;
getLow() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeOrBuilder: required int64 low = 1;
getMarker() - Method in class com.intel.genomicsdb.SilentByteBufferStream: Get marker value
getMutableCallsetMap() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder: map<string, .SampleIDToTileDBIDMap> callset_map = 1;
getName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required string name = 1;
getName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: required string name = 1;
getName() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.ChromosomeOrBuilder: required string name = 1;
getName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string name = 1;
getName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: required string name = 1;
getName() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: required string name = 1;
getNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required string name = 1;
getNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: required string name = 1;
getNameBytes() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.ChromosomeOrBuilder: required string name = 1;
getNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string name = 1;
getNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: required string name = 1;
getNameBytes() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: required string name = 1;
getNumCellsPerTile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 num_cells_per_tile = 16 [default = 1000];
getNumCellsPerTile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional int64 num_cells_per_tile = 16 [default = 1000];
getNumCellsPerTile() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional int64 num_cells_per_tile = 16 [default = 1000];
getNumExhaustedBufferStreams() - Method in class com.intel.genomicsdb.GenomicsDBImporter
getNumParallelVcfFiles() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int32 num_parallel_vcf_files = 9 [default = 1];
getNumParallelVcfFiles() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional int32 num_parallel_vcf_files = 9 [default = 1];
getNumParallelVcfFiles() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional int32 num_parallel_vcf_files = 9 [default = 1];
getNumValidBytes() - Method in class com.intel.genomicsdb.SilentByteBufferStream: Get number of valid bytes
getOffloadVcfOutputProcessing() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool offload_vcf_output_processing = 12 [default = true];
getOffloadVcfOutputProcessing() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool offload_vcf_output_processing = 12 [default = true];
getOffloadVcfOutputProcessing() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool offload_vcf_output_processing = 12 [default = true];
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
getParserForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
getProduceCombinedVcf() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_combined_vcf = 2 [default = false];
getProduceCombinedVcf() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool produce_combined_vcf = 2 [default = false];
getProduceCombinedVcf() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool produce_combined_vcf = 2 [default = false];
getProduceTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_tiledb_array = 3 [default = true];
getProduceTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool produce_tiledb_array = 3 [default = true];
getProduceTiledbArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool produce_tiledb_array = 3 [default = true];
getProgress() - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
getQueryColumnRanges(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRanges(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRanges(int) - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesCount() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesCount() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesCount() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesFieldBuilder() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
getQueryColumnRangesList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesList() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesOrBuilder(int) - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: repeated .ColumnRangeList query_column_ranges = 4;
getQueryColumnRangesOrBuilderList() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: repeated .ColumnRangeList query_column_ranges = 4;
getRangeList(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
getRangeList(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList: repeated .ColumnRange range_list = 1;
getRangeList(int) - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeListOrBuilder: repeated .ColumnRange range_list = 1;
getRangeListBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
getRangeListBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
getRangeListCount() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
getRangeListCount() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList: repeated .ColumnRange range_list = 1;
getRangeListCount() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeListOrBuilder: repeated .ColumnRange range_list = 1;
getRangeListFieldBuilder() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
getRangeListList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
getRangeListList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList: repeated .ColumnRange range_list = 1;
getRangeListList() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeListOrBuilder: repeated .ColumnRange range_list = 1;
getRangeListOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
getRangeListOrBuilder(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList: repeated .ColumnRange range_list = 1;
getRangeListOrBuilder(int) - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeListOrBuilder: repeated .ColumnRange range_list = 1;
getRangeListOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
getRangeListOrBuilderList() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList: repeated .ColumnRange range_list = 1;
getRangeListOrBuilderList() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeListOrBuilder: repeated .ColumnRange range_list = 1;
getReferenceGenome() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string reference_genome = 3;
getReferenceGenome() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string reference_genome = 3;
getReferenceGenome() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string reference_genome = 3;
getReferenceGenomeBytes() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string reference_genome = 3;
getReferenceGenomeBytes() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string reference_genome = 3;
getReferenceGenomeBytes() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string reference_genome = 3;
getRowBasedPartitioning() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool row_based_partitioning = 1 [default = false];
getRowBasedPartitioning() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool row_based_partitioning = 1 [default = false];
getRowBasedPartitioning() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool row_based_partitioning = 1 [default = false];
getSampleName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required string sample_name = 1;
getSampleName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: required string sample_name = 1;
getSampleName() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: required string sample_name = 1;
getSampleNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required string sample_name = 1;
getSampleNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: required string sample_name = 1;
getSampleNameBytes() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: required string sample_name = 1;
getSegmentSize() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 segment_size = 14 [default = 10485760];
getSegmentSize() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional int64 segment_size = 14 [default = 10485760];
getSegmentSize() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional int64 segment_size = 14 [default = 10485760];
getSequenceNames() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader: Return the list of contigs in the combined VCF header
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
getSerializedSize() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
getSizePerColumnPartition() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: required int64 size_per_column_partition = 7 [default = 10240];
getSizePerColumnPartition() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: required int64 size_per_column_partition = 7 [default = 10240];
getSizePerColumnPartition() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: required int64 size_per_column_partition = 7 [default = 10240];
getSplits(JobContext) - Method in class com.intel.genomicsdb.GenomicsDBInputFormat: When this function is called, it is already assumed that configuration object is set
getStreamName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: optional string stream_name = 4;
getStreamName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: optional string stream_name = 4;
getStreamName() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: optional string stream_name = 4;
getStreamNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: optional string stream_name = 4;
getStreamNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: optional string stream_name = 4;
getStreamNameBytes() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: optional string stream_name = 4;
getTiledbArrayName() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_array_name = 2;
getTiledbArrayName() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string tiledb_array_name = 2;
getTiledbArrayName() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string tiledb_array_name = 2;
getTiledbArrayNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_array_name = 2;
getTiledbArrayNameBytes() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string tiledb_array_name = 2;
getTiledbArrayNameBytes() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string tiledb_array_name = 2;
getTiledbColumnOffset() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 tiledb_column_offset = 3;
getTiledbColumnOffset() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: required int64 tiledb_column_offset = 3;
getTiledbColumnOffset() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.ChromosomeOrBuilder: required int64 tiledb_column_offset = 3;
getTiledbRowIndex() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int64 tiledb_row_index = 2;
getTiledbRowIndex() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: required int64 tiledb_row_index = 2;
getTiledbRowIndex() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: required int64 tiledb_row_index = 2;
getTiledbWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_workspace = 1;
getTiledbWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string tiledb_workspace = 1;
getTiledbWorkspace() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string tiledb_workspace = 1;
getTiledbWorkspaceBytes() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_workspace = 1;
getTiledbWorkspaceBytes() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string tiledb_workspace = 1;
getTiledbWorkspaceBytes() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string tiledb_workspace = 1;
getTreatDeletionsAsIntervals() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool treat_deletions_as_intervals = 8 [default = true];
getTreatDeletionsAsIntervals() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool treat_deletions_as_intervals = 8 [default = true];
getTreatDeletionsAsIntervals() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool treat_deletions_as_intervals = 8 [default = true];
getType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string type = 2;
getType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: required string type = 2;
getType() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: required string type = 2;
getTypeBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string type = 2;
getTypeBytes() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: required string type = 2;
getTypeBytes() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: required string type = 2;
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
getUnknownFields() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
getVcfFieldClass(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
getVcfFieldClass(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: repeated string vcf_field_class = 3;
getVcfFieldClass(int) - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: repeated string vcf_field_class = 3;
getVcfFieldClassBytes(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
getVcfFieldClassBytes(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: repeated string vcf_field_class = 3;
getVcfFieldClassBytes(int) - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: repeated string vcf_field_class = 3;
getVcfFieldClassCount() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
getVcfFieldClassCount() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: repeated string vcf_field_class = 3;
getVcfFieldClassCount() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: repeated string vcf_field_class = 3;
getVcfFieldClassList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
getVcfFieldClassList() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: repeated string vcf_field_class = 3;
getVcfFieldClassList() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: repeated string vcf_field_class = 3;
getVcfOutputFilename() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string vcf_output_filename = 4;
getVcfOutputFilename() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string vcf_output_filename = 4;
getVcfOutputFilename() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string vcf_output_filename = 4;
getVcfOutputFilenameBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string vcf_output_filename = 4;
getVcfOutputFilenameBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string vcf_output_filename = 4;
getVcfOutputFilenameBytes() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string vcf_output_filename = 4;
getVidMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string vid_mapping_file = 5;
getVidMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional string vid_mapping_file = 5;
getVidMappingFile() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional string vid_mapping_file = 5;
getVidMappingFileBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string vid_mapping_file = 5;
getVidMappingFileBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional string vid_mapping_file = 5;
getVidMappingFileBytes() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional string vid_mapping_file = 5;
getWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string workspace = 2;
getWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string workspace = 2;
getWorkspace() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string workspace = 2;
getWorkspaceBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string workspace = 2;
getWorkspaceBytes() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string workspace = 2;
getWorkspaceBytes() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string workspace = 2;

H

hasArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string array = 3;
hasArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string array = 3;
hasArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string array = 3;
hasBegin() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: required int64 begin = 1;
hasBegin() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: required int64 begin = 1;
hasBegin() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: required int64 begin = 1;
hasCallsetMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string callset_mapping_file = 6;
hasCallsetMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional string callset_mapping_file = 6;
hasCallsetMappingFile() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional string callset_mapping_file = 6;
hasCompressTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool compress_tiledb_array = 15 [default = true];
hasCompressTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool compress_tiledb_array = 15 [default = true];
hasCompressTiledbArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool compress_tiledb_array = 15 [default = true];
hasDeleteAndCreateTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool delete_and_create_tiledb_array = 10 [default = false];
hasDeleteAndCreateTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool delete_and_create_tiledb_array = 10 [default = false];
hasDeleteAndCreateTiledbArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool delete_and_create_tiledb_array = 10 [default = false];
hasDiscardVcfIndex() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool discard_vcf_index = 13 [default = true];
hasDiscardVcfIndex() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool discard_vcf_index = 13 [default = true];
hasDiscardVcfIndex() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool discard_vcf_index = 13 [default = true];
hasDoPingPongBuffering() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool do_ping_pong_buffering = 11 [default = true];
hasDoPingPongBuffering() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool do_ping_pong_buffering = 11 [default = true];
hasDoPingPongBuffering() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool do_ping_pong_buffering = 11 [default = true];
hasEnd() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional int64 end = 5 [default = 9223372036854775807];
hasEnd() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional int64 end = 5 [default = 9223372036854775807];
hasEnd() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional int64 end = 5 [default = 9223372036854775807];
hasHigh() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 high = 2;
hasHigh() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange: required int64 high = 2;
hasHigh() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeOrBuilder: required int64 high = 2;
hasIdxInFile() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int32 idx_in_file = 3;
hasIdxInFile() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: required int32 idx_in_file = 3;
hasIdxInFile() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: required int32 idx_in_file = 3;
hasIterator() - Method in class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper: Returns true if a non-null Iterator over VariantContext objects was provided for this stream
hasLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 length = 2;
hasLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: required int64 length = 2;
hasLength() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.ChromosomeOrBuilder: required int64 length = 2;
hasLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: optional string length = 4;
hasLength() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: optional string length = 4;
hasLength() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: optional string length = 4;
hasLow() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 low = 1;
hasLow() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange: required int64 low = 1;
hasLow() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeOrBuilder: required int64 low = 1;
hasName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required string name = 1;
hasName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: required string name = 1;
hasName() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.ChromosomeOrBuilder: required string name = 1;
hasName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string name = 1;
hasName() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: required string name = 1;
hasName() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: required string name = 1;
hasNext() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
hasNext() - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
hasNext() - Method in class com.intel.genomicsdb.MultiChromosomeIterator
hasNumCellsPerTile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 num_cells_per_tile = 16 [default = 1000];
hasNumCellsPerTile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional int64 num_cells_per_tile = 16 [default = 1000];
hasNumCellsPerTile() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional int64 num_cells_per_tile = 16 [default = 1000];
hasNumParallelVcfFiles() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int32 num_parallel_vcf_files = 9 [default = 1];
hasNumParallelVcfFiles() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional int32 num_parallel_vcf_files = 9 [default = 1];
hasNumParallelVcfFiles() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional int32 num_parallel_vcf_files = 9 [default = 1];
hasOffloadVcfOutputProcessing() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool offload_vcf_output_processing = 12 [default = true];
hasOffloadVcfOutputProcessing() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool offload_vcf_output_processing = 12 [default = true];
hasOffloadVcfOutputProcessing() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool offload_vcf_output_processing = 12 [default = true];
hasProduceCombinedVcf() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_combined_vcf = 2 [default = false];
hasProduceCombinedVcf() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool produce_combined_vcf = 2 [default = false];
hasProduceCombinedVcf() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool produce_combined_vcf = 2 [default = false];
hasProduceTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_tiledb_array = 3 [default = true];
hasProduceTiledbArray() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool produce_tiledb_array = 3 [default = true];
hasProduceTiledbArray() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool produce_tiledb_array = 3 [default = true];
hasReferenceGenome() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string reference_genome = 3;
hasReferenceGenome() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string reference_genome = 3;
hasReferenceGenome() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string reference_genome = 3;
hasRowBasedPartitioning() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool row_based_partitioning = 1 [default = false];
hasRowBasedPartitioning() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool row_based_partitioning = 1 [default = false];
hasRowBasedPartitioning() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool row_based_partitioning = 1 [default = false];
hasSampleName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required string sample_name = 1;
hasSampleName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: required string sample_name = 1;
hasSampleName() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: required string sample_name = 1;
hasSegmentSize() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 segment_size = 14 [default = 10485760];
hasSegmentSize() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional int64 segment_size = 14 [default = 10485760];
hasSegmentSize() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional int64 segment_size = 14 [default = 10485760];
hasSizePerColumnPartition() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: required int64 size_per_column_partition = 7 [default = 10240];
hasSizePerColumnPartition() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: required int64 size_per_column_partition = 7 [default = 10240];
hasSizePerColumnPartition() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: required int64 size_per_column_partition = 7 [default = 10240];
hasStreamName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: optional string stream_name = 4;
hasStreamName() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: optional string stream_name = 4;
hasStreamName() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: optional string stream_name = 4;
hasTiledbArrayName() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_array_name = 2;
hasTiledbArrayName() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string tiledb_array_name = 2;
hasTiledbArrayName() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string tiledb_array_name = 2;
hasTiledbColumnOffset() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 tiledb_column_offset = 3;
hasTiledbColumnOffset() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: required int64 tiledb_column_offset = 3;
hasTiledbColumnOffset() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.ChromosomeOrBuilder: required int64 tiledb_column_offset = 3;
hasTiledbRowIndex() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int64 tiledb_row_index = 2;
hasTiledbRowIndex() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: required int64 tiledb_row_index = 2;
hasTiledbRowIndex() - Method in interface com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMapOrBuilder: required int64 tiledb_row_index = 2;
hasTiledbWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_workspace = 1;
hasTiledbWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: required string tiledb_workspace = 1;
hasTiledbWorkspace() - Method in interface com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfigurationOrBuilder: required string tiledb_workspace = 1;
hasTreatDeletionsAsIntervals() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool treat_deletions_as_intervals = 8 [default = true];
hasTreatDeletionsAsIntervals() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional bool treat_deletions_as_intervals = 8 [default = true];
hasTreatDeletionsAsIntervals() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional bool treat_deletions_as_intervals = 8 [default = true];
hasType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string type = 2;
hasType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: required string type = 2;
hasType() - Method in interface com.intel.genomicsdb.GenomicsDBVidMapProto.InfoFieldOrBuilder: required string type = 2;
hasVcfOutputFilename() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string vcf_output_filename = 4;
hasVcfOutputFilename() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string vcf_output_filename = 4;
hasVcfOutputFilename() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string vcf_output_filename = 4;
hasVidMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string vid_mapping_file = 5;
hasVidMappingFile() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: optional string vid_mapping_file = 5;
hasVidMappingFile() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfigurationOrBuilder: optional string vid_mapping_file = 5;
hasWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string workspace = 2;
hasWorkspace() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: optional string workspace = 2;
hasWorkspace() - Method in interface com.intel.genomicsdb.GenomicsDBImportConfiguration.PartitionOrBuilder: optional string workspace = 2;
high_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
high_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
HIGH_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
hosts - Variable in class com.intel.genomicsdb.GenomicsDBConfiguration
hosts - Variable in class com.intel.genomicsdb.GenomicsDBInputSplit

I

IDX_IN_FILE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
idxInFile_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
idxInFile_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
importBatch() - Method in class com.intel.genomicsdb.GenomicsDBImporter
ImportConfiguration(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
ImportConfiguration() - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
ImportConfiguration(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
InfoField(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
InfoField() - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
InfoField(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
infofields_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
infofields_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
INFOFIELDS_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
infofieldsBuilder_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
initialize(String, String, FeatureCodec<T, SOURCE>) - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader: Initialization function that's used by all constructors
initialize(String, int, long, long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Initialize variables
initialize(InputSplit, TaskAttemptContext) - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
initialize() - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
initializeSampleInfoMapFromHeader(Map<Integer, SampleInfo>, VCFHeader, long) - Static method in class com.intel.genomicsdb.GenomicsDBImporter: Static function that reads sample names from the vcfHeader and adds entries to the map.
internal_static_CallsetMappingPB_CallsetMapEntry_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
internal_static_CallsetMappingPB_CallsetMapEntry_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
internal_static_CallsetMappingPB_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
internal_static_CallsetMappingPB_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
internal_static_Chromosome_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto
internal_static_Chromosome_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto
internal_static_ColumnRange_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration
internal_static_ColumnRange_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration
internal_static_ColumnRangeList_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration
internal_static_ColumnRangeList_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration
internal_static_ExportConfiguration_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration
internal_static_ExportConfiguration_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration
internal_static_ImportConfiguration_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration
internal_static_ImportConfiguration_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration
internal_static_InfoField_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto
internal_static_InfoField_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto
internal_static_Partition_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration
internal_static_Partition_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration
internal_static_SampleIDToTileDBIDMap_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
internal_static_SampleIDToTileDBIDMap_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
internal_static_VidMappingPB_descriptor - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto
internal_static_VidMappingPB_fieldAccessorTable - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto
internalGetCallsetMap() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
internalGetCallsetMap() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
internalGetFieldAccessorTable() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
internalGetMapField(int) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
internalGetMapField(int) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
internalGetMutableCallsetMap() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
internalGetMutableMapField(int) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
isDone() - Method in class com.intel.genomicsdb.GenomicsDBImporter: Is the import process completed
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
isInitialized() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
iterator() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
iterator() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader: Return an iterator over VariantContext objects for the specified TileDB array and query configuration
iterator - Variable in class com.intel.genomicsdb.GenomicsDBRecordReader

J

jniAddBufferStream(long, String, boolean, long, byte[], long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Notify importer object that a new stream is to be added
jniCopyCallsetMap(long, byte[]) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Copy the callset map protocol buffer to C++ through JNI
jniCopyVidMap(long, byte[]) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Copy the vid map protocol buffer to C++ through JNI
jniGenomicsDBClose(long) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
jniGenomicsDBGetNumBytesAvailable(long) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
jniGenomicsDBImporter(String, int, long, long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Creates GenomicsDBImporter object when importing VCF files (no streams)
jniGenomicsDBInit(String, String, String, int, int, int, long, long) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
jniGenomicsDBOneTimeInitialize() - Static method in class com.intel.genomicsdb.GenomicsDBUtils
jniGenomicsDBRead(long, byte[], int, int) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
jniGenomicsDBReadNextByte(long) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
jniGenomicsDBSkip(long, long) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
jniGetChromosomeIntervalsForColumnPartition(String, int) - Static method in class com.intel.genomicsdb.GenomicsDBImporter: Obtain the chromosome intervals for the column partition specified in the loader JSON file identified by the rank.
jniImportBatch(long, long[]) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Import the next batch of data into TileDB/GenomicsDB
jniInitializeGenomicsDBImporterObject(String, int, long, long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Creates GenomicsDBImporter object when importing VCF files (no streams)
jniSetupGenomicsDBLoader(long, String, boolean) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Setup loader after all the buffer streams are added
jniWriteDataToBufferStream(long, int, int, byte[], long) - Method in class com.intel.genomicsdb.GenomicsDBImporter

L

length - Variable in class com.intel.genomicsdb.GenomicsDBInputSplit
length_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
length_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
length_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
length_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
LENGTH_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
LENGTH_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
LOADERJSON - Static variable in class com.intel.genomicsdb.GenomicsDBConfiguration
loadLibrary() - Static method in class com.intel.genomicsdb.GenomicsDBUtils
loadLibraryFromJar(String) - Static method in class com.intel.genomicsdb.GenomicsDBUtils: Loads library from current JAR archive The file from JAR is copied into system temporary directory and then loaded.
logger - Variable in class com.intel.genomicsdb.GenomicsDBInputFormat
logger - Variable in class com.intel.genomicsdb.GenomicsDBInputSplit
low_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
low_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
LOW_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange

M

main(String[]) - Static method in class com.intel.genomicsdb.GenomicsDBJavaSparkFactory
markSupported() - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
maybeForceBuilderInitialization() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
mBegin - Variable in class com.intel.genomicsdb.ChromosomeInterval
mBeginCpuTime - Variable in class com.intel.genomicsdb.GenomicsDBTimer
mBeginWallClockTime - Variable in class com.intel.genomicsdb.GenomicsDBTimer
mBuffer - Variable in class com.intel.genomicsdb.SilentByteBufferStream
mBufferStreamWrapperVector - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mCallsetMap - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mCallsetMappingJSON - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mChromosomeInterval - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mChromosomeIntervals - Variable in class com.intel.genomicsdb.MultiChromosomeIterator
mChromosomeName - Variable in class com.intel.genomicsdb.ChromosomeInterval
mClosedBefore - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
mCodec - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
mCodec - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader
mContainsBufferStreams - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mCumulativeCpuTime - Variable in class com.intel.genomicsdb.GenomicsDBTimer
mCumulativeWallClockTime - Variable in class com.intel.genomicsdb.GenomicsDBTimer
mCurrentVC - Variable in class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper
mDefaultBufferCapacity - Static variable in class com.intel.genomicsdb.GenomicsDBImporter
mDone - Variable in class com.intel.genomicsdb.GenomicsDBImporter
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
memoizedIsInitialized - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
mEnd - Variable in class com.intel.genomicsdb.ChromosomeInterval
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
mergeFrom(GenomicsDBCallsetsMapProto.CallsetMappingPB) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
mergeFrom(GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
mergeFrom(GenomicsDBExportConfiguration.ColumnRange) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
mergeFrom(GenomicsDBExportConfiguration.ColumnRangeList) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
mergeFrom(GenomicsDBExportConfiguration.ExportConfiguration) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
mergeFrom(GenomicsDBImportConfiguration.ImportConfiguration) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
mergeFrom(GenomicsDBImportConfiguration.Partition) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
mergeFrom(GenomicsDBVidMapProto.Chromosome) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
mergeFrom(GenomicsDBVidMapProto.InfoField) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
mergeFrom(Message) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
mergeFrom(GenomicsDBVidMapProto.VidMappingPB) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
mergeFrom(CodedInputStream, ExtensionRegistryLite) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder
mExhaustedBufferStreamIdentifiers - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mFCHeader - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader
mGenomicsDBImporterObjectHandle - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mGenomicsDBLibraryName - Static variable in class com.intel.genomicsdb.GenomicsDBUtils
mGenomicsDBReadStateHandle - Variable in class com.intel.genomicsdb.GenomicsDBQueryStream
mIdxInIntervalList - Variable in class com.intel.genomicsdb.MultiChromosomeIterator
mIsLibraryLoaded - Static variable in class com.intel.genomicsdb.GenomicsDBUtils
mIsLoaderSetupDone - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mIterator - Variable in class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper
mIterator - Variable in class com.intel.genomicsdb.MultiChromosomeIterator
mLastIntervalCpuTime - Variable in class com.intel.genomicsdb.GenomicsDBTimer
mLastIntervalWallClockTime - Variable in class com.intel.genomicsdb.GenomicsDBTimer
mLbRowIdx - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mLoaderJSONFile - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader
mLoaderJSONFile - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mLoaderJSONFile - Variable in class com.intel.genomicsdb.GenomicsDBQueryStream
mMarker - Variable in class com.intel.genomicsdb.SilentByteBufferStream
mName - Variable in class com.intel.genomicsdb.SampleInfo
mNumExhaustedBufferStreams - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mNumValidBytes - Variable in class com.intel.genomicsdb.SilentByteBufferStream
mOverflow - Variable in class com.intel.genomicsdb.SilentByteBufferStream
MPIHOSTFILE - Static variable in class com.intel.genomicsdb.GenomicsDBConfiguration
mQueryJSONFile - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader
mQueryJSONFile - Variable in class com.intel.genomicsdb.GenomicsDBQueryStream
mRank - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mReader - Variable in class com.intel.genomicsdb.MultiChromosomeIterator
mRowIdx - Variable in class com.intel.genomicsdb.SampleInfo
mSequenceNames - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader
mSource - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
mStream - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
mStream - Variable in class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper
mTempLoaderJSONFileName - Static variable in class com.intel.genomicsdb.GenomicsDBImporter
mTimer - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
mUbRowIdx - Variable in class com.intel.genomicsdb.GenomicsDBImporter
MultiChromosomeIterator<SOURCE> - Class in com.intel.genomicsdb: 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
MultiChromosomeIterator(AbstractFeatureReader<VariantContext, SOURCE>, List<ChromosomeInterval>) - Constructor for class com.intel.genomicsdb.MultiChromosomeIterator: Constructor
mUsingVidMappingProtoBuf - Variable in class com.intel.genomicsdb.GenomicsDBImporter
mVCFHeader - Variable in class com.intel.genomicsdb.GenomicsDBFeatureReader
mVCWriter - Variable in class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper
mVidMap - Variable in class com.intel.genomicsdb.GenomicsDBImporter

N

name_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
name_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
name_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
name_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
NAME_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
NAME_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
nCellsPerTile - Variable in class com.intel.genomicsdb.GenomicsDBConfiguration
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
newBuilder(GenomicsDBCallsetsMapProto.CallsetMappingPB) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
newBuilder(GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
newBuilder(GenomicsDBExportConfiguration.ColumnRange) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
newBuilder(GenomicsDBExportConfiguration.ColumnRangeList) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
newBuilder(GenomicsDBExportConfiguration.ExportConfiguration) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
newBuilder(GenomicsDBImportConfiguration.ImportConfiguration) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
newBuilder(GenomicsDBImportConfiguration.Partition) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
newBuilder(GenomicsDBVidMapProto.Chromosome) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
newBuilder(GenomicsDBVidMapProto.InfoField) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
newBuilder() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
newBuilder(GenomicsDBVidMapProto.VidMappingPB) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
newBuilderForType() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
newBuilderForType(GeneratedMessage.BuilderParent) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
next() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
next() - Method in class com.intel.genomicsdb.GenomicsDBImporterStreamWrapper: Returns the next VariantContext object iff the Iterator over VariantContext objects is non-null and has a next() object, else returns null.
next() - Method in class com.intel.genomicsdb.MultiChromosomeIterator
nextKeyValue() - Method in class com.intel.genomicsdb.GenomicsDBRecordReader
NUM_CELLS_PER_TILE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
NUM_PARALLEL_VCF_FILES_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
numCellsPerTile_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
numCellsPerTile_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
numParallelVcfFiles_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
numParallelVcfFiles_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration

O

OFFLOAD_VCF_OUTPUT_PROCESSING_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
offloadVcfOutputProcessing_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
offloadVcfOutputProcessing_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
overflow() - Method in class com.intel.genomicsdb.SilentByteBufferStream: Returns if the buffer has overflowed

P

parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseDelimitedFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseDelimitedFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
parseFrom(ByteString) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(ByteString, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(byte[]) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(byte[], ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(InputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(InputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(CodedInputStream) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
parseFrom(CodedInputStream, ExtensionRegistryLite) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
PARSER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB: Deprecated.
parser() - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
Partition(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
Partition() - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
Partition(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
PARTITION_STRATEGY - Static variable in class com.intel.genomicsdb.GenomicsDBConfiguration
partitionInfoList - Variable in class com.intel.genomicsdb.GenomicsDBConfiguration
print(String, PrintStream) - Method in class com.intel.genomicsdb.GenomicsDBTimer
printLoaderJSONFile(GenomicsDBImportConfiguration.ImportConfiguration, String) - Static method in class com.intel.genomicsdb.GenomicsDBImporter: Create a JSON file from the import configuration
PRODUCE_COMBINED_VCF_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
PRODUCE_TILEDB_ARRAY_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
produceCombinedVCF - Variable in class com.intel.genomicsdb.GenomicsDBConfiguration
produceCombinedVcf_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
produceCombinedVcf_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
produceTileDBArray - Variable in class com.intel.genomicsdb.GenomicsDBConfiguration
produceTiledbArray_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
produceTiledbArray_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
putAllCallsetMap(Map<String, GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap>) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder: map<string, .SampleIDToTileDBIDMap> callset_map = 1;

Q

query(String, int, int) - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader: Return an iterator over VariantContext objects for the specified TileDB array and queried position
QUERY_COLUMN_RANGES_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
queryColumnRanges_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
queryColumnRanges_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
queryColumnRangesBuilder_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
QUERYJSON - Static variable in class com.intel.genomicsdb.GenomicsDBConfiguration

R

RANGE_LIST_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
rangeList_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
rangeList_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
rangeListBuilder_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder
read() - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
read(byte[], int, int) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
readFields(DataInput) - Method in class com.intel.genomicsdb.GenomicsDBInputSplit
REFERENCE_GENOME_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
referenceGenome_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
referenceGenome_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
registerAllExtensions(ExtensionRegistry) - Static method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto
registerAllExtensions(ExtensionRegistry) - Static method in class com.intel.genomicsdb.GenomicsDBExportConfiguration
registerAllExtensions(ExtensionRegistry) - Static method in class com.intel.genomicsdb.GenomicsDBImportConfiguration
registerAllExtensions(ExtensionRegistry) - Static method in class com.intel.genomicsdb.GenomicsDBVidMapProto
remove() - Method in class com.intel.genomicsdb.GenomicsDBFeatureReader.GenomicsDBFeatureIterator
remove(List<GenomicsDBVidMapProto.InfoField>, int) - Method in class com.intel.genomicsdb.GenomicsDBImporter
removeChromosomes(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
removeColumnPartitions(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
removeInfofields(int) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
removeQueryColumnRanges(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
removeRangeList(int) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
resize(long) - Method in class com.intel.genomicsdb.SilentByteBufferStream: Resizes buffer to new size - data is retained
ROW_BASED_PARTITIONING_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
rowBasedPartitioning_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
rowBasedPartitioning_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration

S

SAMPLE_NAME_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
SampleIDToTileDBIDMap(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
SampleIDToTileDBIDMap() - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
SampleIDToTileDBIDMap(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
SampleInfo - Class in com.intel.genomicsdb: Utility class that stores row index and globally unique name for a given sample
SampleInfo(String, long) - Constructor for class com.intel.genomicsdb.SampleInfo
sampleName_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
sampleName_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
SEGMENT_SIZE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
segmentSize - Variable in class com.intel.genomicsdb.GenomicsDBConfiguration
segmentSize_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
segmentSize_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
serialVersionUID - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
setArray(String) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string array = 3;
setArrayBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string array = 3;
setAttributes(int, String) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated string attributes = 5;
setBegin(long) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: required int64 begin = 1;
setCallsetMappingFile(String) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string callset_mapping_file = 6;
setCallsetMappingFileBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string callset_mapping_file = 6;
setChromosomes(int, GenomicsDBVidMapProto.Chromosome) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
setChromosomes(int, GenomicsDBVidMapProto.Chromosome.Builder) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .Chromosome chromosomes = 2;
setColumnPartitions(int, GenomicsDBImportConfiguration.Partition) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
setColumnPartitions(int, GenomicsDBImportConfiguration.Partition.Builder) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: repeated .Partition column_partitions = 4;
setCompressTiledbArray(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool compress_tiledb_array = 15 [default = true];
setConf(Configuration) - Method in class com.intel.genomicsdb.GenomicsDBInputFormat
setDeleteAndCreateTiledbArray(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool delete_and_create_tiledb_array = 10 [default = false];
setDiscardVcfIndex(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool discard_vcf_index = 13 [default = true];
setDoPingPongBuffering(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool do_ping_pong_buffering = 11 [default = true];
setEnd(long) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional int64 end = 5 [default = 9223372036854775807];
setHigh(long) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 high = 2;
setHostFile(String) - Method in class com.intel.genomicsdb.GenomicsDBConfiguration: Host file contains the hosts where GenomicsDB instances reside.
setHostFile(String) - Method in class com.intel.genomicsdb.GenomicsDBInputFormat: Set the host file path
setIdxInFile(int) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int32 idx_in_file = 3;
setInfofields(int, GenomicsDBVidMapProto.InfoField) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
setInfofields(int, GenomicsDBVidMapProto.InfoField.Builder) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB.Builder: repeated .InfoField infofields = 1;
setLength(long) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 length = 2;
setLength(String) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: optional string length = 4;
setLengthBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: optional string length = 4;
setLoaderJsonFile(String) - Method in class com.intel.genomicsdb.GenomicsDBConfiguration
setLoaderJsonFile(String) - Method in class com.intel.genomicsdb.GenomicsDBInputFormat: Set the loader JSON file path
setLow(long) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange.Builder: required int64 low = 1;
setMarker(long) - Method in class com.intel.genomicsdb.SilentByteBufferStream: Caller code can use this function to mark a certain point in the buffer This is generally used to mark the position in the buffer after the last complete VariantContext object written
setName(String) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required string name = 1;
setName(String) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string name = 1;
setNameBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required string name = 1;
setNameBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string name = 1;
setNumCellsPerTile(long) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 num_cells_per_tile = 16 [default = 1000];
setNumParallelVcfFiles(int) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int32 num_parallel_vcf_files = 9 [default = 1];
setNumValidBytes(long) - Method in class com.intel.genomicsdb.SilentByteBufferStream: Set number of valid bytes
setOffloadVcfOutputProcessing(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool offload_vcf_output_processing = 12 [default = true];
setOverflow(boolean) - Method in class com.intel.genomicsdb.SilentByteBufferStream: Set overflow value
setPartitionStrategy(Boolean) - Method in class com.intel.genomicsdb.GenomicsDBConfiguration: Set the partition strategy for underlying TileDB storage manager
setPartitionStrategy(String) - Method in class com.intel.genomicsdb.GenomicsDBConfiguration: Set the partition strategy for underlying TileDB storage manager
setProduceCombinedVcf(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_combined_vcf = 2 [default = false];
setProduceTiledbArray(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool produce_tiledb_array = 3 [default = true];
setQueryColumnRanges(int, GenomicsDBExportConfiguration.ColumnRangeList) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
setQueryColumnRanges(int, GenomicsDBExportConfiguration.ColumnRangeList.Builder) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: repeated .ColumnRangeList query_column_ranges = 4;
setQueryJsonFile(String) - Method in class com.intel.genomicsdb.GenomicsDBConfiguration
setQueryJsonFile(String) - Method in class com.intel.genomicsdb.GenomicsDBInputFormat: Set the query JSON file path
setRangeList(int, GenomicsDBExportConfiguration.ColumnRange) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
setRangeList(int, GenomicsDBExportConfiguration.ColumnRange.Builder) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList.Builder: repeated .ColumnRange range_list = 1;
setReferenceGenome(String) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string reference_genome = 3;
setReferenceGenomeBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string reference_genome = 3;
setRowBasedPartitioning(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool row_based_partitioning = 1 [default = false];
setSampleName(String) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required string sample_name = 1;
setSampleNameBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required string sample_name = 1;
setSegmentSize(long) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional int64 segment_size = 14 [default = 10485760];
setSizePerColumnPartition(long) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: required int64 size_per_column_partition = 7 [default = 10240];
setSortedVariantContextIterator(String, VCFHeader, Iterator<VariantContext>, long, VariantContextWriterBuilder.OutputType, Map<Integer, SampleInfo>) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Sets sorted VC iterator as the data source and calls setupGenomicsDBImporter().
setStreamName(String) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: optional string stream_name = 4;
setStreamNameBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: optional string stream_name = 4;
setTiledbArrayName(String) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_array_name = 2;
setTiledbArrayNameBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_array_name = 2;
setTiledbColumnOffset(long) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder: required int64 tiledb_column_offset = 3;
setTiledbRowIndex(long) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder: required int64 tiledb_row_index = 2;
setTiledbWorkspace(String) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_workspace = 1;
setTiledbWorkspaceBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder: required string tiledb_workspace = 1;
setTreatDeletionsAsIntervals(boolean) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional bool treat_deletions_as_intervals = 8 [default = true];
setType(String) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string type = 2;
setTypeBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: required string type = 2;
setupGenomicsDBImporter() - Method in class com.intel.genomicsdb.GenomicsDBImporter: Setup the importer after all the buffer streams are added, but before any data is inserted into any stream No more buffer streams can be added once setupGenomicsDBImporter() is called
setVcfFieldClass(int, String) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder: repeated string vcf_field_class = 3;
setVcfOutputFilename(String) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string vcf_output_filename = 4;
setVcfOutputFilenameBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string vcf_output_filename = 4;
setVidMappingFile(String) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string vid_mapping_file = 5;
setVidMappingFileBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder: optional string vid_mapping_file = 5;
setWorkspace(String) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string workspace = 2;
setWorkspaceBytes(ByteString) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder: optional string workspace = 2;
SilentByteBufferStream - Class in com.intel.genomicsdb: 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.
SilentByteBufferStream() - Constructor for class com.intel.genomicsdb.SilentByteBufferStream: Constructor - uses default value of buffer capacity (20KiB)
SilentByteBufferStream(long) - Constructor for class com.intel.genomicsdb.SilentByteBufferStream: Constructor - uses specified buffer capacity
size() - Method in class com.intel.genomicsdb.SilentByteBufferStream: Returns buffer capacity in bytes
SIZE_PER_COLUMN_PARTITION_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
sizePerColumnPartition_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
sizePerColumnPartition_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
skip(long) - Method in class com.intel.genomicsdb.GenomicsDBQueryStream
start() - Method in class com.intel.genomicsdb.GenomicsDBTimer
stop() - Method in class com.intel.genomicsdb.GenomicsDBTimer
STREAM_NAME_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
streamName_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
streamName_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap

T

TILEDB_ARRAY_NAME_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
TILEDB_COLUMN_OFFSET_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
TILEDB_ROW_INDEX_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
TILEDB_WORKSPACE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
tileDBArrayName - Variable in class com.intel.genomicsdb.GenomicsDBPartitionInfo
tiledbArrayName_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
tiledbArrayName_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
tiledbColumnOffset_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome.Builder
tiledbColumnOffset_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
tiledbRowIndex_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder
tiledbRowIndex_ - Variable in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
tileDBWorkspace - Variable in class com.intel.genomicsdb.GenomicsDBPartitionInfo
tiledbWorkspace_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration.Builder
tiledbWorkspace_ - Variable in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
toBuilder() - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
toJSON() - Method in class com.intel.genomicsdb.GenomicsDBPartitionInfo: Create a JSON string from the partition info object
toString() - Method in class com.intel.genomicsdb.GenomicsDBPartitionInfo
TREAT_DELETIONS_AS_INTERVALS_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
treatDeletionsAsIntervals_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
treatDeletionsAsIntervals_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
type_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
type_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
TYPE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField

U

usingGenomicsRDD(String[]) - Static method in class com.intel.genomicsdb.GenomicsDBJavaSparkFactory
usingNewAPIHadoopRDD(String[]) - Static method in class com.intel.genomicsdb.GenomicsDBJavaSparkFactory

V

VCF_FIELD_CLASS_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
VCF_OUTPUT_FILENAME_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
vcfFieldClass_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField.Builder
vcfFieldClass_ - Variable in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
VCFOutputFileName - Variable in class com.intel.genomicsdb.GenomicsDBPartitionInfo
vcfOutputFilename_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
vcfOutputFilename_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
VID_MAPPING_FILE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
vidMappingFile_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration.Builder
vidMappingFile_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
VidMappingPB(GeneratedMessage.Builder<?>) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
VidMappingPB() - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB
VidMappingPB(CodedInputStream, ExtensionRegistryLite) - Constructor for class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB

W

workspace_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition.Builder
workspace_ - Variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
WORKSPACE_FIELD_NUMBER - Static variable in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
write() - Method in class com.intel.genomicsdb.GenomicsDBImporter: Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
write(long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
write(int, long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
write(int, long, long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
write(String, int, long, long) - Method in class com.intel.genomicsdb.GenomicsDBImporter: Write to TileDB/GenomicsDB
write(DataOutput) - Method in class com.intel.genomicsdb.GenomicsDBInputSplit
write(byte[], int, int) - Method in class com.intel.genomicsdb.SilentByteBufferStream
write(byte[]) - Method in class com.intel.genomicsdb.SilentByteBufferStream
write(int) - Method in class com.intel.genomicsdb.SilentByteBufferStream
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.CallsetMappingPB
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRange
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ColumnRangeList
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBExportConfiguration.ExportConfiguration
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.ImportConfiguration
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBImportConfiguration.Partition
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.Chromosome
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.InfoField
writeTo(CodedOutputStream) - Method in class com.intel.genomicsdb.GenomicsDBVidMapProto.VidMappingPB

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