| Interface | Description |
|---|---|
| VCFIDHeaderLine |
an interface for ID-based header lines
|
| VCFIterator |
An iterator of `VariantContext`.
|
| VCFReader |
Interface for reading VCF/BCF files.
|
| VCFTextTransformer |
Interface for transforming attribute values embedded in 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)
|
| 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
|
| VCFHeaderLine | |
| VCFHeaderLineTranslator |
A class for translating between vcf header versions
|
| VCFInfoHeaderLine | |
| 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.
|
| 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
|
| VCFUtils |
| Enum | Description |
|---|---|
| VCFCompoundHeaderLine.SupportedHeaderLineType | |
| VCFHeader.HEADER_FIELDS | |
| VCFHeaderLineCount |
the count encodings we use for fields in VCF header lines
|
| VCFHeaderLineType |
the type encodings we use for fields in VCF header lines
|
| VCFHeaderVersion |
information that identifies each header version
|