Package main

Class RunStats

java.lang.Object
main.RunStats
public class RunStats extends Object

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

Instances of class RunStats are not thread-safe.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    duoPrintNanos(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(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, FixedPhaseData fpd)
    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 Details

    • 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:
      NullPointerException - if this.par().ped() != null && ped == null

    • printWindowUpdate

      public void printWindowUpdate(Window window, FixedPhaseData fpd)
      Prints information about the marker window to a log file and to standard output.
      Parameters:
      window - input data for the next marker window
      fpd - the input data for phasing that is the same in each iteration
      Throws:
      NullPointerException - if (window == null) || (fpd == null)

    • 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(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(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