Package de.charite.compbio.jannovar.htsjdk

Class Summary

Class	Description
GenomeRegionSequenceExtractor	Extract sequence for a GenomeInterval from a IndexedFastaSequenceFile.
VariantContextAnnotator	Helper class for generating VariantAnnotations objects from VariantContexts.
VariantContextAnnotator.Options	Options class for VariantContextAnnotator.
VariantContextWriterConstructionHelper	Helper for creating a VariantContextWriter from a OutputStream.
VariantEffectHeaderExtender	Code for adding headers for variant effect to VCF files

Exception Summary

Exception	Description
InvalidBreakendDescriptionException	Thrown in VariantContextAnnotator in the case of invalid breakend descriptions.
InvalidCoordinatesException	Thrown in VariantContextAnnotator in the case of invalid positions (unknown chromsomes).
MissingEndInfoField	Thrown in VariantContextAnnotator in the case missing END in the INFO field.
MissingSVTypeInfoField	Thrown in VariantContextAnnotator in the case missing SVTYPE in the INFO field.
MixingSmallAndSVAlleles	Thrown in VariantContextAnnotator in the case of mixing small and SV alleles.
MultipleSVAlleles	Thrown in VariantContextAnnotator in the case of having more than one SV allele in a variant.