java.lang.Object
- main.Par

```
public final class Par
extends java.lang.Object
```
Class Parameters represents the parameters for a Beagle analysis.

Instances of class Parameters are immutable.

Constructor Summary

Constructors
Constructor Description

Par(java.lang.String[] args)
Constructs a new Parameters instance from the specified command line arguments.

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 or `null` if no chrom parameter was specified.
`float`	`cluster()`	Returns the cluster parameter.
`boolean`	`em()`	Returns the em parameter.
`float`	`err(int nHaps)`	Returns the default allele mismatch parameter for the specified number of haplotypes.
`java.io.File`	`excludemarkers()`	Returns the excludemarkers parameter or `null` if no excludemarkers parameter was specified.
`java.io.File`	`excludesamples()`	Returns the excludesamples parameter or `null` if no excludesamples parameter was specified.
`boolean`	`gp()`	Returns the gp parameter.
`java.io.File`	`gt()`	Returns the gt parameter or `null` 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.
`static float`	`liStephensPMismatch(int nHaps)`	Return an approximation to the allele mismatch probability suggested by Li and Stephens.
`java.io.File`	`map()`	Returns the map parameter.
`float`	`ne()`	Returns the ne parameter
`boolean`	`noNThreads()`	Returns `true` if the command line does not include an nthreads parameter and returns `false otherwise`.
`int`	`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 or `null` if no ped parameter was specified.
`int`	`phase_states()`	Returns the phase-states parameter.
`float`	`rare()`	Returns the rare parameter
`java.io.File`	`ref()`	Returns the ref parameter or `null` if no ref parameter was specified.
`long`	`seed()`	Returns the seed parameter.
`float`	`step_scale()`	Returns the step-scale parameter.
`java.io.File`	`truth()`	Returns the truth parameter
`static java.lang.String`	`usage()`	Returns a description of the Beagle command line arguments.
`float`	`window()`	Returns the window parameter.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - Par
```
public Par(java.lang.String[] args)
```
    Constructs a new Parameters instance from the specified command line arguments.
    
    Parameters:
    
    args - the command line arguments
    
    Throws:
    
    java.lang.IllegalArgumentException - if a command line argument is incorrectly specified
    
    java.lang.NumberFormatException - if a numeric value for a parameter is incorrectly specified
    
    java.lang.NullPointerException - if args == null
- Method Detail
  - args
```
public java.lang.String[] args()
```
    Returns the command line arguments.
    
    Returns:
    
    the command line arguments
  - noNThreads
```
public boolean noNThreads()
```
    Returns true if the command line does not include an nthreads parameter and returns false otherwise.
    
    Returns:
    
    true if the command line does not include an nthreads parameter
  - 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
  - gt
```
public java.io.File gt()
```
    Returns the gt parameter or null if no gt parameter was specified.
    
    Returns:
    
    the gt parameter or null if no gt parameter was specified
  - ref
```
public java.io.File ref()
```
    Returns the ref parameter or null if no ref parameter was specified.
    
    Returns:
    
    the ref parameter or null if no ref parameter was specified
  - out
```
public java.lang.String out()
```
    Returns the out parameter.
    
    Returns:
    
    the out parameter
  - ped
```
public java.io.File ped()
```
    Returns the ped parameter or null if no ped parameter was specified.
    
    Returns:
    
    the ped parameter or null if no ped parameter was specified
  - map
```
public java.io.File map()
```
    Returns the map parameter.
    
    Returns:
    
    the map parameter
  - chromInt
```
public ChromInterval chromInt()
```
    Returns the chromosome interval or null if no chrom parameter was specified.
    
    Returns:
    
    the chromosome interval or null if no chrom parameter was specified.
  - excludesamples
```
public java.io.File excludesamples()
```
    Returns the excludesamples parameter or null if no excludesamples parameter was specified.
    
    Returns:
    
    the excludesamples parameter or null if no excludesamples parameter was specified
  - excludemarkers
```
public java.io.File excludemarkers()
```
    Returns the excludemarkers parameter or null if no excludemarkers parameter was specified.
    
    Returns:
    
    the excludemarkers parameter or null if no excludemarkers parameter was specified
  - burnin
```
public int burnin()
```
    Returns the burnin parameter.
    
    Returns:
    
    the burnin parameter
  - iterations
```
public int iterations()
```
    Returns the iterations parameter.
    
    Returns:
    
    the iterations parameter
  - phase_states
```
public int phase_states()
```
    Returns the phase-states parameter.
    
    Returns:
    
    the phase-states parameter
  - step_scale
```
public float step_scale()
```
    Returns the step-scale parameter.
    
    Returns:
    
    the step-scale parameter
  - rare
```
public float rare()
```
    Returns the rare parameter
    
    Returns:
    
    the rare parameter
  - impute
```
public boolean impute()
```
    Returns the impute parameter.
    
    Returns:
    
    the impute parameter
  - imp_states
```
public int imp_states()
```
    Returns the imp-states parameter.
    
    Returns:
    
    the imp-states parameter
  - imp_segment
```
public float imp_segment()
```
    Returns the imp-segment parameter.
    
    Returns:
    
    the imp-segment parameter
  - imp_step
```
public float imp_step()
```
    Returns the imp-step parameter.
    
    Returns:
    
    the imp-step parameter
  - imp_nsteps
```
public int imp_nsteps()
```
    Returns the imp-nsteps parameter.
    
    Returns:
    
    the imp-nsteps parameter
  - cluster
```
public float cluster()
```
    Returns the cluster parameter.
    
    Returns:
    
    the cluster parameter
  - ap
```
public boolean ap()
```
    Returns the ap parameter.
    
    Returns:
    
    the ap parameter
  - gp
```
public boolean gp()
```
    Returns the gp parameter.
    
    Returns:
    
    the gp parameter
  - em
```
public boolean em()
```
    Returns the em parameter.
    
    Returns:
    
    the em parameter
  - ne
```
public float ne()
```
    Returns the ne parameter
    
    Returns:
    
    the ne parameter
  - err
```
public float err(int nHaps)
```
    Returns the default allele mismatch parameter for the specified number of haplotypes.
    
    Parameters:
    
    nHaps - the number of reference and target haplotypes
    
    Returns:
    
    the default allele mismatch parameter for the specified number of haplotypes
  - liStephensPMismatch
```
public static float liStephensPMismatch(int nHaps)
```
    Return an approximation to the allele mismatch probability suggested by Li and Stephens. The approximation uses a Riemann sum approximation of the natural log function.
    
    Refs: Li N, Stephens M. Genetics 2003 Dec;165(4):2213-33 and Marchini J, Howie B. Myers S, McVean G, Donnelly P. 2007;39(7):906-13.
    
    Parameters:
    
    nHaps - the number of haplotypes
    
    Returns:
    
    the allele mismatch probability suggested by Li and Stepehens
  - window
```
public float window()
```
    Returns the window parameter.
    
    Returns:
    
    the window parameter
  - overlap
```
public float overlap()
```
    Return the overlap parameter.
    
    Returns:
    
    the overlap parameter.
  - buffer
```
public float buffer()
```
    Return the buffer parameter.
    
    Returns:
    
    the buffer parameter.
  - seed
```
public long seed()
```
    Returns the seed parameter.
    
    Returns:
    
    the seed parameter
  - nthreads
```
public int nthreads()
```
    Returns the nthreads parameter.
    
    Returns:
    
    the nthreads parameter
  - truth
```
public java.io.File truth()
```
    Returns the truth parameter
    
    Returns:
    
    the truth

Class Par

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Par

Method Detail

args

noNThreads

usage

gt

ref

out

ped

map

chromInt

excludesamples

excludemarkers

burnin

iterations

phase_states

step_scale

rare

impute

imp_states

imp_segment

imp_step

imp_nsteps

cluster

ap

gp

em

ne

err

liStephensPMismatch

window

overlap

buffer

seed

nthreads

truth