Uses of Class
com.intel.genomicsdb.ChromosomeInterval

Uses of ChromosomeInterval in com.intel.genomicsdb

Fields in com.intel.genomicsdb declared as ChromosomeInterval

Modifier and Type	Field and Description
private ChromosomeInterval	GenomicsDBImporter.mChromosomeInterval

Fields in com.intel.genomicsdb with type parameters of type ChromosomeInterval

Modifier and Type	Field and Description
private ArrayList<ChromosomeInterval>	MultiChromosomeIterator.mChromosomeIntervals

Methods in com.intel.genomicsdb that return types with arguments of type ChromosomeInterval

Modifier and Type	Method and Description
private static ArrayList<ChromosomeInterval>	GenomicsDBImporter.getChromosomeIntervalsForColumnPartition(String loaderJSONFile, int partitionIdx) Utility function that returns a list of ChromosomeInterval objects for the column partition specified by the loader JSON file and rank/partition index

Constructors in com.intel.genomicsdb with parameters of type ChromosomeInterval

Constructor and Description
GenomicsDBImporter(Map<String,htsjdk.tribble.FeatureReader<htsjdk.variant.variantcontext.VariantContext>> sampleToVCMap, Set<htsjdk.variant.vcf.VCFHeaderLine> mergedHeader, ChromosomeInterval chromosomeInterval, String workspace, String arrayname, Long sizePerColumnPartition, Long segmentSize) Constructor to create required data structures from a list of GVCF files and a chromosome interval.
GenomicsDBImporter(Map<String,htsjdk.tribble.FeatureReader<htsjdk.variant.variantcontext.VariantContext>> sampleToVCMap, Set<htsjdk.variant.vcf.VCFHeaderLine> mergedHeader, ChromosomeInterval chromosomeInterval, String workspace, String arrayname, Long sizePerColumnPartition, Long segmentSize, boolean useSamplesInOrderProvided) Constructor to create required data structures from a list of GVCF files and a chromosome interval.
GenomicsDBImporter(Map<String,htsjdk.tribble.FeatureReader<htsjdk.variant.variantcontext.VariantContext>> sampleToVCMap, Set<htsjdk.variant.vcf.VCFHeaderLine> mergedHeader, ChromosomeInterval chromosomeInterval, String workspace, String arrayname, Long sizePerColumnPartition, Long segmentSize, String outputVidMapJSONFilePath) Constructor to create required data structures from a list of GVCF files and a chromosome interval.

Constructor parameters in com.intel.genomicsdb with type arguments of type ChromosomeInterval

Constructor and Description
MultiChromosomeIterator(htsjdk.tribble.AbstractFeatureReader<htsjdk.variant.variantcontext.VariantContext,SOURCE> reader, List<ChromosomeInterval> chromosomeIntervals) Constructor