public class RunStats
extends java.lang.Object
RunStats
contains methods for storing and printing
statistics describing a Beagle analysis.Modifier and Type | Method and Description |
---|---|
void |
buildNanos(long nanos)
Increases the cumulative time to build the DAG models by the
specified number of nanoseconds.
|
void |
ibdNanos(long nanos)
Increases the cumulative time for detecting identity-by-descent
by the specified number of nanoseconds.
|
void |
imputationNanos(long nanos)
Stores the time for imputing ungenotyped marker and increases
the cumulative imputation 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 |
printRefinedIbdUpdate(float ibdScale,
Dag ibdDag,
long nanos)
Prints information about the Refined IBD analysis to a log
file and to standard output.
|
void |
printSampleSummary(NuclearFamilies fam,
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.
|
void |
sampleNanos(long nanos)
Stores the time for sampling new haplotypes and increases the
cumulative sampling time by the specified number of nanoseconds.
|
void |
setDagStats(Dag dag)
Stores statistics for the DAG model used to sample single individuals.
|
public void printStartInfo()
public 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 sampleNanos(long nanos)
nanos
- the nanoseconds required to sample new haplotypespublic void imputationNanos(long nanos)
nanos
- the nanoseconds required to impute ungenotyped
markerspublic void ibdNanos(long nanos)
nanos
- the nanoseconds required to perform IBD detectionpublic void setDagStats(Dag dag)
dag
- the DAG model used to sample individualspublic void printRefinedIbdUpdate(float ibdScale, Dag ibdDag, long nanos)
ibdScale
- the value used to multiplicatively scales the node
similarity threshold when building the DAG modelibdDag
- the DAG model used for IBD detectionnanos
- the nanoseconds required for IBD detectionjava.lang.NullPointerException
- if ibdDag == null
public void printImputationUpdate()
public void printSampleSummary(NuclearFamilies fam, Data data)
fam
- the parent-offspring relationshipsdata
- the input genotype datapublic void printWindowUpdate(Data data)
data
- the input genotype datapublic void println(java.lang.String msg)
msg
- the message to be printedpublic void printIterationUpdate(int window, int iter)
window
- the windowiter
- the iteration