Class Fields

The Fields class represents a collection of VCF (Variant Call Format) header information fields. These Fields are stored in VariantDatabase / VariantDataFrame objects, that are used to annotate VCF files. It provides methods to manipulate and retrieve field values from VCF entries. This class implements the Iterable interface to allow iteration over VcfHeaderInfo objects. It also implements Serializable to allow instances to be serialized and deserialized. Fields are stored in a Map with their names as keys and VcfHeaderInfo objects as values. The class provides methods to add fields, retrieve field values, and save/load the Fields object to/from a file. Limitations: - The class cannot use REF/ALT fields directly because they are used to separate variant types in the database. - INFO and FORMAT fields are not appropriate to be stuffed into an INFO field. - The class assumes that certain VCF columns (e.g., CHROM, POS, ID, QUAL, FILTER) are implicitly present and handles them separately. - The getFieldValue method handles different VCF info types (Flag, Integer, Float, Character, String) and converts values accordingly. - The class does not handle all possible VCF info types and throws a RuntimeException for unimplemented types.