• AlignmentToSamRecord
• AlignmentToSamRecordFactory
• GenotypesToVariantContext
• GenotypesToVariantContextFactory
• HtsjdkModule
• SamHeaderToProcessingSteps
• SamHeaderToReadGroups
• SamHeaderToReferences
• SamProgramRecordToProcessingStep
• SamReadGroupRecordToReadGroup
• SamRecordToAlignment
• SamSequenceRecordToReference
• VariantContextToGenotypes
• VariantContextToGenotypesFactory
• VariantContextToVariants
• VariantContextToVariantsFactory
• VariantToVariantContext
• VariantToVariantContextFactory
• VcfHeaderToReferences
• VcfHeaderToSamples
• VcfHeaderToVcfHeaderLines