Package main
Class Par
- java.lang.Object
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- main.Par
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public final class Par extends java.lang.Object
Class
Parameters
represents the parameters for a Beagle analysis.Instances of class
Parameters
are immutable.
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Constructor Summary
Constructors Constructor Description Par(java.lang.String[] args)
Constructs a newParameters
instance from the specified command line arguments.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
ap()
Returns the ap parameter.java.lang.String[]
args()
Returns the command line arguments.float
buffer()
Return the buffer parameter.int
burnin()
Returns the burnin parameter.ChromInterval
chromInt()
Returns the chromosome interval ornull
if no chrom parameter was specified.float
cluster()
Returns the cluster parameter.float
err(int nHaps)
Returns the allele mismatch parameter for the specified number of samples.java.io.File
excludemarkers()
Returns the excludemarkers parameter ornull
if no excludemarkers parameter was specified.java.io.File
excludesamples()
Returns the excludesamples parameter ornull
if no excludesamples parameter was specified.boolean
gp()
Returns the gp parameter.java.io.File
gt()
Returns the gt parameter ornull
if no gt parameter was specified.int
imp_nsteps()
Returns the imp-nsteps parameter.float
imp_segment()
Returns the imp-segment parameter.int
imp_states()
Returns the imp-states parameter.float
imp_step()
Returns the imp-step parameter.boolean
impute()
Returns the impute parameter.int
iterations()
Returns the iterations parameter.java.io.File
map()
Returns the map parameter.float
ne()
Returns the ne parameterint
nthreads()
Returns the nthreads parameter.java.lang.String
out()
Returns the out parameter.float
overlap()
Return the overlap parameter.java.io.File
ped()
Returns the ped parameter ornull
if no ped parameter was specified.int
phase_states()
Returns the phase-states parameter.float
phase_step()
Returns the phase-step parameter.float
rare()
Returns the rare parameterjava.io.File
ref()
Returns the ref parameter ornull
if no ref parameter was specified.float
scaleFactor()
Return the ratio of the phase-states parameter and the default phase-states parameterlong
seed()
Returns the seed parameter.java.io.File
truth()
Returns the truth parameterstatic java.lang.String
usage()
Returns a description of the Beagle command line arguments.float
window()
Returns the window parameter.
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Constructor Detail
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Par
public Par(java.lang.String[] args)
Constructs a newParameters
instance from the specified command line arguments.- Parameters:
args
- the command line arguments- Throws:
java.lang.IllegalArgumentException
- if a command line argument is incorrectly specifiedjava.lang.NumberFormatException
- if a numeric value for a parameter is incorrectly specifiedjava.lang.NullPointerException
- ifargs == null
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Method Detail
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args
public java.lang.String[] args()
Returns the command line arguments.- Returns:
- the command line arguments
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usage
public static java.lang.String usage()
Returns a description of the Beagle command line arguments.- Returns:
- a description of the Beagle command line arguments
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gt
public java.io.File gt()
Returns the gt parameter ornull
if no gt parameter was specified.- Returns:
- the gt parameter or
null
if no gt parameter was specified
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ref
public java.io.File ref()
Returns the ref parameter ornull
if no ref parameter was specified.- Returns:
- the ref parameter or
null
if no ref parameter was specified
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out
public java.lang.String out()
Returns the out parameter.- Returns:
- the out parameter
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ped
public java.io.File ped()
Returns the ped parameter ornull
if no ped parameter was specified.- Returns:
- the ped parameter or
null
if no ped parameter was specified
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map
public java.io.File map()
Returns the map parameter.- Returns:
- the map parameter
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chromInt
public ChromInterval chromInt()
Returns the chromosome interval ornull
if no chrom parameter was specified.- Returns:
- the chromosome interval or
null
if no chrom parameter was specified.
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excludesamples
public java.io.File excludesamples()
Returns the excludesamples parameter ornull
if no excludesamples parameter was specified.- Returns:
- the excludesamples parameter or
null
if no excludesamples parameter was specified
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excludemarkers
public java.io.File excludemarkers()
Returns the excludemarkers parameter ornull
if no excludemarkers parameter was specified.- Returns:
- the excludemarkers parameter or
null
if no excludemarkers parameter was specified
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burnin
public int burnin()
Returns the burnin parameter.- Returns:
- the burnin parameter
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iterations
public int iterations()
Returns the iterations parameter.- Returns:
- the iterations parameter
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phase_states
public int phase_states()
Returns the phase-states parameter.- Returns:
- the phase-states parameter
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scaleFactor
public float scaleFactor()
Return the ratio of the phase-states parameter and the default phase-states parameter- Returns:
- the ratio of the phase-states parameter and the default phase-states parameter
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phase_step
public float phase_step()
Returns the phase-step parameter.- Returns:
- the phase-step parameter
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rare
public float rare()
Returns the rare parameter- Returns:
- the rare parameter
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impute
public boolean impute()
Returns the impute parameter.- Returns:
- the impute parameter
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imp_states
public int imp_states()
Returns the imp-states parameter.- Returns:
- the imp-states parameter
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imp_segment
public float imp_segment()
Returns the imp-segment parameter.- Returns:
- the imp-segment parameter
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imp_step
public float imp_step()
Returns the imp-step parameter.- Returns:
- the imp-step parameter
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imp_nsteps
public int imp_nsteps()
Returns the imp-nsteps parameter.- Returns:
- the imp-nsteps parameter
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cluster
public float cluster()
Returns the cluster parameter.- Returns:
- the cluster parameter
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ap
public boolean ap()
Returns the ap parameter.- Returns:
- the ap parameter
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gp
public boolean gp()
Returns the gp parameter.- Returns:
- the gp parameter
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ne
public float ne()
Returns the ne parameter- Returns:
- the ne parameter
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err
public float err(int nHaps)
Returns the allele mismatch parameter for the specified number of samples.- Parameters:
nHaps
- the number of reference and target haplotypes- Returns:
- the allele mismatch parameter for the specified number of samples
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window
public float window()
Returns the window parameter.- Returns:
- the window parameter
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overlap
public float overlap()
Return the overlap parameter.- Returns:
- the overlap parameter.
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buffer
public float buffer()
Return the buffer parameter.- Returns:
- the buffer parameter.
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seed
public long seed()
Returns the seed parameter.- Returns:
- the seed parameter
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nthreads
public int nthreads()
Returns the nthreads parameter.- Returns:
- the nthreads parameter
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truth
public java.io.File truth()
Returns the truth parameter- Returns:
- the truth
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