Package main

Class RunStats

  • public class RunStats
extends java.lang.Object

    Class RunStats contains methods for storing and printing statistics describing a Beagle analysis.

    Instances of class RunStats are not thread-safe.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      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.
      Par par()
      Returns the analysis parameters.
      void phaseNanos​(long nanos)
      Increases the cumulative phasing time by the specified number of nanoseconds.
      void printEstimatedParameters​(long ne, float pMismatch)
      Prints the specified estimated effective population size.
      void printImputationUpdate()
      Prints run time for most recent imputation to a log file and to standard output.
      void println​(java.lang.String msg)
      Prints the specified string to the log file and to standard out.
      void printSampleSummary​(Pedigree ped, Window window)
      Prints information about the samples to a log file and to standard output.
      void printStage1Info​(PhaseData pd, long elapsedNanos)
      Prints information about the specified iteration, and adds the specified elapsed nanoseconds to the total phasing time.
      void printStage2Info​(long elapsedNanos)
      Prints the specified elapsed nanoseconds for stage 2 phasing.
      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​(Window window)
      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.

      • par

        public Par par()
        Returns the analysis parameters.
        Returns:
        the analysis parameters

      • printSampleSummary

        public void printSampleSummary​(Pedigree ped,
                               Window window)
        Prints information about the samples to a log file and to standard output.
        Parameters:
        ped - the pedigree data for the target samples
        window - the input data for the current marker window
        Throws:
        java.lang.NullPointerException - if this.par().ped() != null && ped == null

      • printWindowUpdate

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

      • 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

      • phaseNanos

        public void phaseNanos​(long nanos)
        Increases the cumulative phasing time by the specified number of nanoseconds.
        Parameters:
        nanos - the elapsed nanoseconds for 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

      • printStage1Info

        public void printStage1Info​(PhaseData pd,
                            long elapsedNanos)
        Prints information about the specified iteration, and adds the specified elapsed nanoseconds to the total phasing time.
        Parameters:
        pd - estimated phased genotypes at stage 1 markers
        elapsedNanos - the elapsed nanoseconds for the iteration

      • printStage2Info

        public void printStage2Info​(long elapsedNanos)
        Prints the specified elapsed nanoseconds for stage 2 phasing.
        Parameters:
        elapsedNanos - the elapsed nanoseconds for stage 2 phasing

      • printEstimatedParameters

        public void printEstimatedParameters​(long ne,
                                     float pMismatch)
        Prints the specified estimated effective population size.
        Parameters:
        ne - the estimated effective population size
        pMismatch - the estimated allele mismatch parameter

      • 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