Package VCF

Class Genotype


  • public class Genotype
    extends java.lang.Object
    Represents a single genotype in a VCF file
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void addData​(java.lang.String value)
      Add data to the genotype.
      Genotype copy()
      Create a copy of the genotype
      java.lang.String getData()
      Get all the data associated with this genotype
      java.lang.String getData​(java.lang.String name)
      Get a specified piece of data for this genotype.
      PositionMeta getPositionMeta()
      Get the position metadata for the position associated with this genotype
      java.lang.String getSampleName()
      Get the sample name for the name associated with this genotype
      void removeData​(java.lang.String name)
      Remove data for the given format.
      void replaceData​(java.lang.String name, java.lang.String value)
      Change a particular piece of data associated with the genotype
      java.lang.String toString()  
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, wait, wait, wait
    • Method Detail

      • getPositionMeta

        public PositionMeta getPositionMeta()
        Get the position metadata for the position associated with this genotype
        Returns:
        Position metadata
      • getSampleName

        public java.lang.String getSampleName()
        Get the sample name for the name associated with this genotype
        Returns:
        The sample name
      • getData

        public java.lang.String getData()
        Get all the data associated with this genotype
        Returns:
        The data as a string
      • getData

        public java.lang.String getData​(java.lang.String name)
                                 throws VCFNoDataException
        Get a specified piece of data for this genotype. Returns "." if field is not present for this genotype.
        Parameters:
        name - The format of the data to be retrieved (as a string)
        Returns:
        The data
        Throws:
        VCFNoDataException - If there is a no data for the requested format
      • replaceData

        public void replaceData​(java.lang.String name,
                                java.lang.String value)
                         throws VCFNoDataException
        Change a particular piece of data associated with the genotype
        Parameters:
        name - The format of the data to be changed (as a string)
        value - The new value
        Throws:
        VCFNoDataException - If there is a no data for the requested format
      • addData

        public void addData​(java.lang.String value)
        Add data to the genotype. It is up to the caller to ensure the appropriate format is also added to the position.
        Parameters:
        value - The value to add
      • removeData

        public void removeData​(java.lang.String name)
                        throws VCFNoDataException
        Remove data for the given format. It is up to the caller to ensure the appropriate format is removed from the position.
        Parameters:
        name - The name of the format data to remove
        Throws:
        VCFNoDataException - If there is no data field with that name
      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
      • copy

        public Genotype copy()
        Create a copy of the genotype
        Returns:
        A copy of the genotype