Package Executable

Class PrintStats


  • public class PrintStats
    extends java.lang.Object
    Class used to print stats
    • Constructor Summary

      Constructors 
      Constructor Description
      PrintStats​(java.io.File pretty, java.io.File depth, java.io.File geno, java.io.File depthGeno, java.io.File eachMasked, boolean partial)
      Constructor
      PrintStats​(java.lang.String root, boolean partial)
      Constructor that creates file names for the different output based on a root string
      PrintStats​(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
      Constructor from a config (read in from a XML file)
    • Constructor Detail

      • PrintStats

        public PrintStats​(java.io.File pretty,
                          java.io.File depth,
                          java.io.File geno,
                          java.io.File depthGeno,
                          java.io.File eachMasked,
                          boolean partial)
        Constructor
        Parameters:
        pretty - File to print pretty stats to
        depth - File to print depth stats to
        geno - File to print geno stats to
        depthGeno - File to print depth-geno stats to
        eachMasked - File to print information for each masked sample / position to
        partial - Whether to print partial stats (i.e. for imputed and called as well as for combined)
      • PrintStats

        public PrintStats​(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
      • PrintStats

        public PrintStats​(java.lang.String root,
                          boolean partial)
        Constructor that creates file names for the different output based on a root string
        Parameters:
        root - The root string
        partial - Whether to print partial stats (i.e. for imputed and called as well as for combined)
    • Method Detail

      • writeEachMasked

        public void writeEachMasked​(java.util.List<SingleGenotypeCall> correct,
                                    java.util.List<SingleGenotypeCall> imputed,
                                    java.lang.String[] samples,
                                    PositionMeta[] positions)
                             throws OutputException
        Writes data on each masked sample / snp if appropriate
        Parameters:
        correct - List of correct genotypes
        imputed - List of imputed genotypes
        samples - List of samples (sample names)
        positions - List of positions (position meta data)
        Throws:
        OutputException - If there is an IO problem
      • getConfig

        public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
        Get the imputer options config
        Returns:
        The config