Package main
Class RunStats
- java.lang.Object
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- main.RunStats
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public class RunStats extends java.lang.Object
ClassRunStats
contains methods for storing and printing statistics describing a Beagle analysis.
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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 byblbutil.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.
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Method Detail
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printStartInfo
public void printStartInfo()
Prints initial information about the analysis to a log file and to standard output.
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printSampleSummary
public void printSampleSummary(Data data)
Prints information about the samples to a log file and to standard output.- Parameters:
data
- the input data
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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
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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 analyzednMarkers
- the total number of markers analyzed
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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
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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
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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
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printImputationUpdate
public void printImputationUpdate()
Prints run time for most recent imputation to a log file and to standard output.
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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
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printIterationUpdate
public void printIterationUpdate(int window, int iter)
Prints information about the specified iteration.- Parameters:
window
- the windowiter
- the iteration
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printPhasingIterationUpdate
public void printPhasingIterationUpdate(int it, boolean burnin, long elapsedNanos)
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duoPrintNanos
public void duoPrintNanos(java.lang.String message, long nanos)
Print the specified message followed by the human elapsed time as formatted byblbutil.Utilities.elapsedNanos(nanos)
- Parameters:
message
- the message to be printednanos
- the elapsed time in nanoseconds
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