Package VCF.Filters

Class HasDepthFilter

  • All Implemented Interfaces:
    VCFFilter

    public class HasDepthFilter
    extends PositionFilter
    Filter positions that do not have depth data
    • Constructor Summary

      Constructors 
      Constructor Description
      HasDepthFilter()
      Constructor
      HasDepthFilter​(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

      • HasDepthFilter

        public HasDepthFilter()
        Constructor
      • HasDepthFilter

        public HasDepthFilter​(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)
        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
      • 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