Package Executable

Class Input


  • public class Input
    extends java.lang.Object
    Represents the input to LinkImputeR
    • Constructor Summary

      Constructors 
      Constructor Description
      Input​(java.io.File in, java.util.List<PositionFilter> filters, java.io.File out, int maxdepth, java.lang.String readsformat)
      Constructor
      Input​(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 input config
      org.apache.commons.configuration2.tree.ImmutableNode getImputeConfig()
      Get the input config for the final imputation step
      VCF getVCF()
      Get the VCF data
      • Methods inherited from class java.lang.Object

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

      • Input

        public Input​(java.io.File in,
                     java.util.List<PositionFilter> filters,
                     java.io.File out,
                     int maxdepth,
                     java.lang.String readsformat)
        Constructor
        Parameters:
        in - The input VCF file
        filters - The filters to apply to the VCF as it is read in
        out - The file to output the VCF to IMMEDIATELY after the VCF has been read in and the input parameters applied. Input filters are applied in all cases so it can save time in the final imputation step to save a VCF with the filters applied rather than read it in from scratch and reapply the filters.
        maxdepth - The maximum read depth for a genotype. Genotypes with a higher read depth are set to have no reads and a missing genotype.
        readsformat - The formats to read read depths from. If a single value then assumes the format contains comma separated data for reference alt read depths. If readsformat is itself comma seperated then assumes the first item is the format containing the reference allele depth, the second the alt allele depth. If null defaults to the current VCF standard (AD).
      • Input

        public Input​(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

      • getConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Get the input config
        Returns:
        The config
      • getImputeConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getImputeConfig()
        Get the input config for the final imputation step
        Returns:
        The config