| Class | Description |
|---|---|
| ChromosomeInterval |
Utility class to represent a chromosome interval
Contains 3 members - chr name, start, end (1-based)
|
| GenomicsDBCallsetsMapProto | |
| GenomicsDBCallsetsMapProto.CallsetMappingPB |
Protobuf type
CallsetMappingPB |
| GenomicsDBCallsetsMapProto.CallsetMappingPB.Builder |
Protobuf type
CallsetMappingPB |
| GenomicsDBCallsetsMapProto.CallsetMappingPB.CallsetMapDefaultEntryHolder | |
| GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap |
Protobuf type
SampleIDToTileDBIDMap |
| GenomicsDBCallsetsMapProto.SampleIDToTileDBIDMap.Builder |
Protobuf type
SampleIDToTileDBIDMap |
| GenomicsDBConfiguration |
The configuration class enables users to use Java/Scala
to populate the input parameters of GenomicsDB.
|
| GenomicsDBExportConfiguration | |
| GenomicsDBExportConfiguration.ColumnRange |
Protobuf type
ColumnRange |
| GenomicsDBExportConfiguration.ColumnRange.Builder |
Protobuf type
ColumnRange |
| GenomicsDBExportConfiguration.ColumnRangeList |
Protobuf type
ColumnRangeList |
| GenomicsDBExportConfiguration.ColumnRangeList.Builder |
Protobuf type
ColumnRangeList |
| GenomicsDBExportConfiguration.ExportConfiguration |
Protobuf type
ExportConfiguration |
| GenomicsDBExportConfiguration.ExportConfiguration.Builder |
Protobuf type
ExportConfiguration |
| GenomicsDBFeatureReader<T extends htsjdk.tribble.Feature,SOURCE> |
A reader for GenomicsDB that implements
FeatureReader
Currently, the reader only return VariantContext |
| GenomicsDBImportConfiguration | |
| GenomicsDBImportConfiguration.ImportConfiguration |
Protobuf type
ImportConfiguration |
| GenomicsDBImportConfiguration.ImportConfiguration.Builder |
Protobuf type
ImportConfiguration |
| GenomicsDBImportConfiguration.Partition |
Protobuf type
Partition |
| GenomicsDBImportConfiguration.Partition.Builder |
Protobuf type
Partition |
| GenomicsDBImporter |
Java wrapper for vcf2tiledb - imports VCFs into TileDB/GenomicsDB.
|
| GenomicsDBImporterStreamWrapper |
Utility class wrapping a stream and a VariantContextWriter for a given stream
Each GenomicsDB import stream consists of a buffer stream and a writer object
If the caller provides an iterator, then mCurrentVC points to the VariantContext
object to be written, if any.
|
| GenomicsDBInputFormat<VCONTEXT extends htsjdk.tribble.Feature,SOURCE> | |
| GenomicsDBInputSplit | |
| GenomicsDBJavaSparkFactory |
This factory class exposes the two ways JavaRDD of variant contexts (htsjdk)
can be retrieved from GenomicsDB.
|
| GenomicsDBPartitionInfo |
Maintain global information on how variant data is partitioned
across multiple nodes (if loaded with mpiexec)
The assumption is that every object described one partition as:
{"begin": 0, "workspace":"/home/forall/tiledb-ws",
"array": "test0", "vcf_output_filename":"/home/forall/lihao/mytest/test0.vcf.gz" }
|
| GenomicsDBQueryStream |
Provides a java.io.InputStream interface for the GenomicsDB combine gVCF operation.
|
| GenomicsDBRecordReader<VCONTEXT extends htsjdk.tribble.Feature,SOURCE> | |
| GenomicsDBTimer | |
| GenomicsDBUtils |
Utility Java functions for GenomicsDB
|
| GenomicsDBVidMapProto | |
| GenomicsDBVidMapProto.Chromosome |
Protobuf type
Chromosome |
| GenomicsDBVidMapProto.Chromosome.Builder |
Protobuf type
Chromosome |
| GenomicsDBVidMapProto.InfoField |
Protobuf type
InfoField |
| GenomicsDBVidMapProto.InfoField.Builder |
Protobuf type
InfoField |
| GenomicsDBVidMapProto.VidMappingPB |
Protobuf type
VidMappingPB |
| GenomicsDBVidMapProto.VidMappingPB.Builder |
Protobuf type
VidMappingPB |
| MultiChromosomeIterator<SOURCE> |
Given an AbstractFeatureReader over VariantContext objects
and a list of ChromosomeInterval objects, this class
is an Iterator over VariantContext for all the chromosome intervals in the
list
|
| SampleInfo |
Utility class that stores row index and globally unique name for a given sample
|
| SilentByteBufferStream |
Buffer stream implementation - it's silent in the sense that when the buffer is full,
it doesn't raise an exception but just marks a a flag as full.
|
| Exception | Description |
|---|---|
| GenomicsDBException |
Classes in the genomicsdb package throw exceptions of type GenomicsDBException
|
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