All Classes and Interfaces
Class
Description
A strictly validated VCF metadata ALT code of the form:
##ALT=<ID=type,Description=description>
Where ID is a colon-delimited list of identifiers.VCF metadata in the format XXX=<key=value,key=value,...>.
VCF metadata for contig=<> elements.
This class represents a single VCF FORMAT metadata line.
This enum represents the Type field in a VCF FORMAT metadata line.
This class represents a single VCF metadata line with an id and description.
A VCF metadata element with an Id (called "ID").
This class represents a single VCF INFO metadata line.
This enum represents the Type field in a VCF INFO metadata line.
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
What to do when a duplicate VCF record (line) is encountered.
A FORMAT field specified as reserved in the VCF specification.
An INFO field specified as reserved in the VCF specification.
A field specified as reserved in the VCF specification.
A reserved identifier for VCF ALT codes of structural variants.
A reserved value for the "Number" field in INFO and FORMAT metadata entries.
Applies a transformation to a VCF file.
An Allele matching the VCF 4.2 specification for the ALT and REF columns.
This exception indicates a VCF format error was found while parsing the VCF file.
A diploid (or haploid; see below) genotype matching the VCF 4.2 specification.
This interface controls what is actually done for each data line in a VCF file.
This class captures all the VCF metadata from a VCF file.
This class parses a VCF file.
This class contains the basic data (the first 9 columns) for a VCF position line.
This class contains sample data for a VCF position line.
A transformation applied to VCF data lines and metadata.
Contains static methods for handling properties in INFO and FORMAT fields.