| Interface | Description |
|---|---|
| VcfLineParser |
This interface controls what is actually done for each data line in a VCF file.
|
| VcfTransformation |
A transformation applied to VCF data lines and metadata.
|
| Class | Description |
|---|---|
| MemoryMappedVcfDataStore | |
| MemoryMappedVcfDataStore.Genotype | |
| MemoryMappedVcfDataStore.Locus | |
| MemoryMappedVcfLineParser |
A simple
VcfLineParser that loads an entire VCF file into memory to permit
constant-time lookup for VCF records, either:
By any ID listed in the ID field, or
By chromosome and position
|
| MemoryMappedVcfLineParser.Builder | |
| TransformingVcfLineParser |
Applies a transformation to a VCF file.
|
| TransformingVcfLineParser.Builder | |
| VcfParser |
This class parses a VCF file.
|
| VcfParser.Builder | |
| VcfUtils |
Contains static methods for handling properties in INFO and FORMAT fields.
|
| VcfWriter | |
| VcfWriter.Builder |
| Enum | Description |
|---|---|
| MemoryMappedVcfLineParser.DuplicateHandler |
What to do when a duplicate VCF record (line) is encountered.
|