Package org.bdgenomics.convert.htsjdk
Convert between htsjdk and bdg-formats data models.
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Interface Summary Interface Description AlignmentToSamRecordFactory Factory for creating Alignment to htsjdk SAMRecord converters, which require late binding for a SAMFileHeader.GenotypesToVariantContextFactory Factory for creating list of Genotypes to VariantContext converters, which require late binding for a VCFHeader.VariantContextToGenotypesFactory Factory for creating VariantContext to list of Genotypes converters, which require late binding for a VCFHeader.VariantContextToVariantsFactory Factory for creating VariantContext to list of Variants converters, which require late binding for a VCFHeader.VariantToVariantContextFactory Factory for creating Variant to VariantContext converters, which require late binding for a VCFHeader. -
Class Summary Class Description AlignmentToSamRecord Convert Alignment to htsjdk SAMRecord.GenotypesToVariantContext Convert a list of Genotypes to a VariantContext.HtsjdkModule Guice module for the org.bdgenomics.convert.htsjdk package.SamHeaderToProcessingSteps Convert a SAMFileHeader to a list of ProcessingSteps.SamHeaderToReadGroups Convert a SAMFileHeader to a list of ReadGroups.SamHeaderToReferences Convert a SAMFileHeader to a list of References.SamProgramRecordToProcessingStep Convert a SAMProgramRecord to a ProcessingStep.SamReadGroupRecordToReadGroup Convert a SAMReadGroup to a ReadGroup.SamRecordToAlignment Convert htsjdk SAMRecord to Alignment.SamSequenceRecordToReference Convert a SAMSequenceRecord to a Reference.VariantContextToGenotypes Convert VariantContext to a list of Genotypes.VariantContextToVariants Convert VariantContext to a list of Variants.VariantToVariantContext Convert a Variant to a VariantContext.VcfHeaderToReferences Convert a VCFHeader to a list of References.VcfHeaderToSamples Convert a VCFHeader to a list of Samples.VcfHeaderToVcfHeaderLines Convert a VCFHeader to a list of VCFHeaderLines.