public class RunStats
extends java.lang.Object
RunStats
contains methods for storing and printing
statistics describing a Beagle analysis.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.
|
public void printStartInfo()
public void printSampleSummary(Data data)
data
- the input datapublic void printWindowUpdate(Data data)
data
- the input genotype datapublic void printSummaryAndClose(int nTargetMarkers, int nMarkers)
nTargetMarkers
- the total number of target markers analyzednMarkers
- the total number of markers analyzedpublic void buildNanos(long nanos)
nanos
- the nanoseconds required to build an instance
of the DAG modelpublic void iterationNanos(long nanos)
nanos
- the nanoseconds required to updating the haplotype
estimatespublic void imputationNanos(long nanos)
nanos
- the nanoseconds required to impute ungenotyped
markerspublic void printImputationUpdate()
public void println(java.lang.String msg)
msg
- the message to be printedpublic void printIterationUpdate(int window, int iter)
window
- the windowiter
- the iterationpublic void printPhasingIterationUpdate(int it, boolean burnin, long elapsedNanos)
public void duoPrintNanos(java.lang.String message, long nanos)
blbutil.Utilities.elapsedNanos(nanos)
message
- the message to be printednanos
- the elapsed time in nanoseconds