All Classes

Class	Description
BaiWriteOption	An option for for enabling or disabling writing BAI files.
CraiWriteOption	An option for for enabling or disabling writing CRAI files.
DisqKryoRegistrator	Kryo registrator for Disq.
FileCardinalityWriteOption	An option for configuring whether to write output in a single file, or multiple files.
HtsjdkReadsRdd	A HtsjdkReadsRdd is the distributed equivalent of a htsjdk SamReader.
HtsjdkReadsRddStorage	The entry point for reading or writing a HtsjdkReadsRdd.
HtsjdkReadsTraversalParameters<T extends htsjdk.samtools.util.Locatable>	Holds parameters controlling which reads get returned when reading a HtsjdkReadsRdd.
HtsjdkVariantsRdd	A HtsjdkVariantsRdd is the distributed equivalent of a htsjdk VCFFileReader.
HtsjdkVariantsRddStorage	The entry point for reading or writing a HtsjdkVariantsRdd.
ReadsFormatWriteOption	An option for configuring which format to write a HtsjdkReadsRdd as.
SbiWriteOption	An option for for enabling or disabling writing SBI files.
TabixIndexWriteOption	An option for for enabling or disabling writing tabix files.
TempPartsDirectoryWriteOption	An option for controlling which directory to write temporary part files to when writing output as a single file.
VariantsFormatWriteOption	An option for configuring which format to write a HtsjdkVariantsRdd as.
WriteOption	An option for configuring how to write output.