Class VcfHeaderInfo

  • Direct Known Subclasses:
    VcfHeaderFormat

    public class VcfHeaderInfo
    extends VcfHeaderEntry
    Represents a info elements in a VCF file References: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 INFO fields should be described as follows (all keys are required): ##INFO= Possible Types for INFO fields are: Integer, Float, Flag, Character, and String. The Number entry is an Integer that describes the number of values that can be included with the INFO field. For example, if the INFO field contains a single number, then this value should be 1; if the INFO field describes a pair of numbers, then this value should be 2 and so on. If the field has one value per alternate allele then this value should be 'A'; if the field has one value for each possible genotype (more relevant to the FORMAT tags) then this value should be 'G'. If the number of possible values varies, is unknown, or is unbounded, then this value should be '.'. The 'Flag' type indicates that the INFO field does not contain a Value entry, and hence the Number should be 0 in this case. The Description value must be surrounded by double-quotes. Double-quote character can be escaped with backslash (\") and backslash as \\.
    Author:
    pablocingolani
    • Field Detail

      • number

        protected int number
      • implicit

        protected boolean implicit
      • description

        protected java.lang.String description
    • Constructor Detail

      • VcfHeaderInfo

        public VcfHeaderInfo​(java.lang.String line)
        Constructor using a "##INFO" line from a VCF file
      • VcfHeaderInfo

        public VcfHeaderInfo​(java.lang.String id,
                             VcfInfoType vcfInfoType,
                             java.lang.String number,
                             java.lang.String description)
    • Method Detail

      • getDescription

        public java.lang.String getDescription()
      • getNumber

        public int getNumber()
      • isImplicit

        public boolean isImplicit()
      • isNumberAllAlleles

        public boolean isNumberAllAlleles()
      • isNumberNumber

        public boolean isNumberNumber()
      • isNumberOnePerAllele

        public boolean isNumberOnePerAllele()
      • isNumberOnePerGenotype

        public boolean isNumberOnePerGenotype()
      • isNumberPerAllele

        public boolean isNumberPerAllele()
      • setImplicit

        public void setImplicit​(boolean implicit)
      • setNumber

        public void setNumber​(int number)
      • setNumber

        public void setNumber​(java.lang.String number)
      • setVcfInfoType

        public void setVcfInfoType​(VcfInfoType vcfInfoType)