Class VcfHeaderInfo

java.lang.Object
org.snpeff.vcf.VcfHeaderEntry
org.snpeff.vcf.VcfHeaderInfo
All Implemented Interfaces:
Serializable
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=invalid input: '<'ID=ID,Number=number,Type=type,Description=description> 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
See Also:
  • Field Details

    • number

      protected int number
    • implicit

      protected boolean implicit
    • vcfInfoNumber

      protected VcfHeaderInfo.VcfInfoNumber vcfInfoNumber
    • vcfInfoType

      protected VcfInfoType vcfInfoType
    • description

      protected String description
  • Constructor Details

    • VcfHeaderInfo

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

      public VcfHeaderInfo(String id, VcfInfoType vcfInfoType, String number, String description)
    • VcfHeaderInfo

      public VcfHeaderInfo(VcfHeaderInfo header)
  • Method Details

    • getDescription

      public String getDescription()
    • getNumber

      public int getNumber()
    • getNumberString

      public String getNumberString()
    • getVcfInfoNumber

      public VcfHeaderInfo.VcfInfoNumber getVcfInfoNumber()
    • getVcfInfoType

      public VcfInfoType getVcfInfoType()
    • isImplicit

      public boolean isImplicit()
    • isInfo

      public boolean isInfo()
      Overrides:
      isInfo in class VcfHeaderEntry
    • 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(String number)
    • setVcfInfoNumber

      public void setVcfInfoNumber(VcfHeaderInfo.VcfInfoNumber vcfInfoNumber)
    • setVcfInfoType

      public void setVcfInfoType(VcfInfoType vcfInfoType)
    • toString

      public String toString()
      Overrides:
      toString in class VcfHeaderEntry