Package main

Class RunStats


  • public class RunStats
    extends java.lang.Object
    Class RunStats contains methods for storing and printing statistics describing a Beagle analysis.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void buildNanos​(long nanos)
      Increases the cumulative time to build the DAG models by the specified number of nanoseconds.
      void duoPrintNanos​(java.lang.String message, long nanos)
      Print the specified message followed by the human elapsed time as formatted by blbutil.Utilities.elapsedNanos(nanos)
      void imputationNanos​(long nanos)
      Stores the time for imputing ungenotyped marker and increases the cumulative imputation time by the specified number of nanoseconds.
      void iterationNanos​(long nanos)
      Stores the time for updating the haplotype estimates and increases the cumulative phasing time by the specified number of nanoseconds.
      void printImputationUpdate()
      Prints run time for most recent imputation to a log file and to standard output.
      void printIterationUpdate​(int window, int iter)
      Prints information about the specified iteration.
      void println​(java.lang.String msg)
      Prints the specified string to the log file and to standard out.
      void printPhasingIterationUpdate​(int it, boolean burnin, long elapsedNanos)  
      void printSampleSummary​(Data data)
      Prints information about the samples to a log file and to standard output.
      void printStartInfo()
      Prints initial information about the analysis to a log file and to standard output.
      void printSummaryAndClose​(int nTargetMarkers, int nMarkers)
      Prints information about the complete analysis to a log file and to standard output, and closes the log file.
      void printWindowUpdate​(Data data)
      Prints information about the marker window to a log file and to standard output.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Method Detail

      • printStartInfo

        public void printStartInfo()
        Prints initial information about the analysis to a log file and to standard output.
      • printSampleSummary

        public void printSampleSummary​(Data data)
        Prints information about the samples to a log file and to standard output.
        Parameters:
        data - the input data
      • printWindowUpdate

        public void printWindowUpdate​(Data data)
        Prints information about the marker window to a log file and to standard output.
        Parameters:
        data - the input genotype data
      • printSummaryAndClose

        public void printSummaryAndClose​(int nTargetMarkers,
                                         int nMarkers)
        Prints information about the complete analysis to a log file and to standard output, and closes the log file.
        Parameters:
        nTargetMarkers - the total number of target markers analyzed
        nMarkers - the total number of markers analyzed
      • buildNanos

        public void buildNanos​(long nanos)
        Increases the cumulative time to build the DAG models by the specified number of nanoseconds.
        Parameters:
        nanos - the nanoseconds required to build an instance of the DAG model
      • iterationNanos

        public void iterationNanos​(long nanos)
        Stores the time for updating the haplotype estimates and increases the cumulative phasing time by the specified number of nanoseconds.
        Parameters:
        nanos - the nanoseconds required to updating the haplotype estimates
      • imputationNanos

        public void imputationNanos​(long nanos)
        Stores the time for imputing ungenotyped marker and increases the cumulative imputation time by the specified number of nanoseconds.
        Parameters:
        nanos - the nanoseconds required to impute ungenotyped markers
      • printImputationUpdate

        public void printImputationUpdate()
        Prints run time for most recent imputation to a log file and to standard output.
      • println

        public void println​(java.lang.String msg)
        Prints the specified string to the log file and to standard out.
        Parameters:
        msg - the message to be printed
      • printIterationUpdate

        public void printIterationUpdate​(int window,
                                         int iter)
        Prints information about the specified iteration.
        Parameters:
        window - the window
        iter - the iteration
      • printPhasingIterationUpdate

        public void printPhasingIterationUpdate​(int it,
                                                boolean burnin,
                                                long elapsedNanos)
      • duoPrintNanos

        public void duoPrintNanos​(java.lang.String message,
                                  long nanos)
        Print the specified message followed by the human elapsed time as formatted by blbutil.Utilities.elapsedNanos(nanos)
        Parameters:
        message - the message to be printed
        nanos - the elapsed time in nanoseconds