public final class Par
extends java.lang.Object
Class Parameters
represents the parameters for a Beagle analysis.
Instances of class Parameters
are immutable.
Constructor | Description |
---|---|
Par(java.lang.String[] args) |
Constructs a new
Parameters instance from the specified
command line arguments. |
Modifier and Type | Method | Description |
---|---|---|
boolean |
ap() |
Returns the ap parameter.
|
java.lang.String[] |
args() |
Returns the command line arguments.
|
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.
|
float |
err() |
Returns the err parameter.
|
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. |
float |
imp_segment() |
Returns the imp-segment parameter.
|
int |
imp_states() |
Returns the imp-states 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 parameter
|
int |
nsteps() |
Returns the nsteps parameter.
|
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. |
float |
phase_segment() |
Returns the phase-segment parameter.
|
int |
phase_states() |
Returns the phase-states 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() |
Returns the step 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.
|
public Par(java.lang.String[] args)
Parameters
instance from the specified
command line arguments.args
- the command line argumentsjava.lang.IllegalArgumentException
- if a command line argument
is incorrectly specifiedjava.lang.NumberFormatException
- if a numeric value for a parameter
is incorrectly specifiedjava.lang.NullPointerException
- if args == null
public java.lang.String[] args()
public static java.lang.String usage()
public java.io.File gt()
null
if no gt parameter was
specified.null
if no gt parameter was
specifiedpublic java.io.File ref()
null
if no ref parameter was
specified.null
if no ref parameter was
specifiedpublic java.lang.String out()
public java.io.File ped()
null
if no ped parameter was specified.null
if no ped parameter was specifiedpublic java.io.File map()
public ChromInterval chromInt()
null
if no chrom
parameter was specified.null
if no chrom
parameter was specified.public java.io.File excludesamples()
null
if no excludesamples parameter was specified.null
if no excludesamples parameter was specifiedpublic java.io.File excludemarkers()
null
if no excludemarkers parameter was specified.null
if no excludemarkers parameter was specifiedpublic int burnin()
public int iterations()
public int phase_states()
public float phase_segment()
public boolean impute()
public int imp_states()
public float imp_segment()
public float cluster()
public boolean ap()
public boolean gp()
public float ne()
public float err()
public float window()
public float overlap()
public long seed()
public int nthreads()
public float step()
public int nsteps()
public java.io.File truth()