Package VCF.Filters

Class MAFFilter

  • All Implemented Interfaces:
    VCFFilter

    public class MAFFilter
    extends PositionFilter
    Filters positions based on minor allele frequency
    • Constructor Summary

      Constructors 
      Constructor Description
      MAFFilter​(double maf, int minDepth, int maxDepth, Caller caller)
      Constructor
      MAFFilter​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
      Constructor from a config (read in from a XML file)
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      org.apache.commons.configuration2.tree.ImmutableNode getConfig()
      Get the config for this filter
      java.lang.String getSummary()
      Gets a string summary of this filter
      boolean test​(Position p)
      Tests whether a position should be filtered out
      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • MAFFilter

        public MAFFilter​(double maf,
                         int minDepth,
                         int maxDepth,
                         Caller caller)
        Constructor
        Parameters:
        maf - Minor allele frequency
        minDepth - A genotype must have at least this number of reads to be used in the MAF calculation
        maxDepth - A genotype must have less than (or equal) this number of reads to be used in the MAF calculation
        caller - The caller to be used when calling genotypes
      • MAFFilter

        public MAFFilter​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
        Constructor from a config (read in from a XML file)
        Parameters:
        params - The config
    • Method Detail

      • test

        public boolean test​(Position p)
                     throws VCFDataException
        Description copied from class: PositionFilter
        Tests whether a position should be filtered out
        Specified by:
        test in class PositionFilter
        Parameters:
        p - The position to test
        Returns:
        Whether this position should be filtered out
        Throws:
        VCFDataException - If there is a problem with the data in the VCF
      • getConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Description copied from interface: VCFFilter
        Get the config for this filter
        Returns:
        The config
      • getSummary

        public java.lang.String getSummary()
        Description copied from interface: VCFFilter
        Gets a string summary of this filter
        Returns:
        The string