Package org.bdgenomics.convert.htsjdk

Convert between htsjdk and bdg-formats data models.

See: Description

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.

Package org.bdgenomics.convert.htsjdk Description

Convert between htsjdk and bdg-formats data models.