Uses of Class
com.intel.genomicsdb.GenomicsDBException

Uses of GenomicsDBException in com.intel.genomicsdb

Methods in com.intel.genomicsdb that throw GenomicsDBException

Modifier and Type	Method and Description
boolean	GenomicsDBImporter.add(htsjdk.variant.variantcontext.VariantContext vc, int streamIdx) 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
private int	GenomicsDBImporter.addBufferStream(String streamName, htsjdk.variant.vcf.VCFHeader vcfHeader, long bufferCapacity, htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType streamType, Iterator<htsjdk.variant.variantcontext.VariantContext> vcIterator, Map<Integer,SampleInfo> sampleIndexToInfo) Add a buffer stream or VC iterator - internal function
int	GenomicsDBImporter.addBufferStream(String streamName, htsjdk.variant.vcf.VCFHeader vcfHeader, long bufferCapacity, htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType streamType, Map<Integer,SampleInfo> sampleIndexToInfo) Add a buffer stream as the data source - caller must: 1.
int	GenomicsDBImporter.addSortedVariantContextIterator(String streamName, htsjdk.variant.vcf.VCFHeader vcfHeader, Iterator<htsjdk.variant.variantcontext.VariantContext> vcIterator, long bufferCapacity, htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType streamType, Map<Integer,SampleInfo> sampleIndexToInfo) Add a sorted VC iterator as the data source - caller must: 1.
int	GenomicsDBImporter.setSortedVariantContextIterator(String streamName, htsjdk.variant.vcf.VCFHeader vcfHeader, Iterator<htsjdk.variant.variantcontext.VariantContext> vcIterator, long bufferCapacity, htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType streamType, Map<Integer,SampleInfo> sampleIndexToInfo) Sets sorted VC iterator as the data source and calls setupGenomicsDBImporter().
void	GenomicsDBImporter.write() Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
void	GenomicsDBImporter.write(int rank, long lbRowIdx) Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
void	GenomicsDBImporter.write(int rank, long lbRowIdx, long ubRowIdx) Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
void	GenomicsDBImporter.write(long lbRowIdx) Write to TileDB/GenomicsDB using the configuration specified in the loader file passed to constructor
void	GenomicsDBImporter.write(String loaderJSONFile, int rank, long lbRowIdx, long ubRowIdx) Write to TileDB/GenomicsDB

Constructors in com.intel.genomicsdb that throw GenomicsDBException

Constructor and Description
GenomicsDBImporterStreamWrapper(htsjdk.variant.vcf.VCFHeader vcfHeader, long bufferCapacity, htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.OutputType streamType, Iterator<htsjdk.variant.variantcontext.VariantContext> vcIterator) Constructor