Package VCF.Filters

Class SampleMissing

  • All Implemented Interfaces:
    VCFFilter

    public class SampleMissing
    extends SampleFilter
    Filters a sample based on a maximum allowed amount of missing genotypes
    • Constructor Summary

      Constructors 
      Constructor Description
      SampleMissing​(double threshold, int minDepth)
      Constructor
      SampleMissing​(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​(Sample s)
      Tests whether a sample should be filtered out
      • Methods inherited from class java.lang.Object

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

      • SampleMissing

        public SampleMissing​(double threshold,
                             int minDepth)
        Constructor
        Parameters:
        threshold - The missing threshold
        minDepth - The minimum number of reads required for a genotype to be considered present
      • SampleMissing

        public SampleMissing​(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​(Sample s)
                     throws VCFDataException
        Description copied from class: SampleFilter
        Tests whether a sample should be filtered out
        Specified by:
        test in class SampleFilter
        Parameters:
        s - The sample to test
        Returns:
        Whether this sample 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