# Package htsjdk.variant.vcf

package htsjdk.variant.vcf

Class
Description
AbstractVCFCodec
VCF3Codec
A feature codec for the VCF3 specification, to read older VCF files.
VCFAltHeaderLine
A class representing ALT fields in the VCF header
VCFCodec
A feature codec for the VCF 4 specification
VCFCompoundHeaderLine
a base class for compound header lines, which include info lines and format lines (so far)
VCFCompoundHeaderLine.SupportedHeaderLineType
VCFConstants
VCFContigHeaderLine
A special class representing a contig VCF header line.
VCFEncoder
Functions specific to encoding VCF records.
VCFFileReader
Simplified interface for reading from VCF/BCF files.
VCFFilterHeaderLine
VCFFormatHeaderLine
VCFHeader
A class to represent a VCF header
VCFHeader.HEADER_FIELDS
VCFHeaderLine
VCFHeaderLineCount
the count encodings we use for fields in VCF header lines
VCFHeaderLineTranslator
A class for translating between vcf header versions
VCFHeaderLineType
the type encodings we use for fields in VCF header lines
VCFHeaderVersion
information that identifies each header version
VCFIDHeaderLine
an interface for ID-based header lines
VCFInfoHeaderLine
VCFIterator
An iterator of `VariantContext`.
VCFIteratorBuilder
A Class building `VCFIterator` Example:
VCFMetaHeaderLine
A class representing META fields in the VCF header
VCFPassThruTextTransformer
A no-op implementation of VCFTextTransformer for pre-v43 VCFs, when such encodings are not supported and no transformation need be done.
VCFPedigreeHeaderLine
A class representing PEDIGREE fields in the VCF header
VCFPercentEncodedTextTransformer
Text transformer for attribute values embedded in VCF.
VCFReader
Interface for reading VCF/BCF files.
VCFRecordCodec
Writes VariantContext instances to an OutputStream without headers or metadata.
VCFSampleHeaderLine
A class representing SAMPLE fields in the VCF header
VCFSimpleHeaderLine
VCFStandardHeaderLines
Manages header lines for standard VCF
VCFTextTransformer
Interface for transforming attribute values embedded in VCF.
VCFUtils