public final class Par
extends java.lang.Object
Class Parameters
represents the parameters for a Beagle analysis.
Instances of class Parameters
are immutable.
Constructor and Description |
---|
Par(java.lang.String[] args)
Constructs a new
Parameters instance from the specified
command line arguments. |
Modifier and Type | Method and Description |
---|---|
float |
adjustedIbdScale(int nSamples)
Returns a sample-size-adjusted IBD scale parameter equal to
Math.max(2.0f, (float) Math.sqrt(nSamples/100.0)) if
this.ibdscale() == 0f , and returns
this.ibdscale() otherwise. |
java.lang.String[] |
args()
Returns the Beagle command line arguments.
|
int |
burnin_its()
Returns the burnin-its parameter.
|
java.lang.String |
chrom()
Returns the chrom parameter or
null
if no chrom parameter was specified. |
float |
cluster()
Returns the cluster parameter.
|
java.io.File |
dag()
Returns the dag parameter or
null if no ref parameter was
specified. |
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. |
java.io.File |
gl()
Returns the gl parameter or
null if no gl parameter was
specified. |
boolean |
gprobs()
Returns the gprobs parameter.
|
java.io.File |
gt()
Returns the gt parameter or
null if no gt parameter was
specified. |
java.io.File |
gtgl()
Returns the gtgl parameter or
null if no gtgl parameter was
specified. |
boolean |
ibd()
Returns the ibd parameter.
|
float |
ibdextend()
Returns the ibdextend parameter.
|
float |
ibdlength()
Returns the ibdlength parameter.
|
float |
ibdlod()
Returns the ibdlod parameter.
|
float |
ibdscale()
Returns the ibdscale parameter.
|
int |
ibdtrim()
Returns the ibdtrim parameter.
|
boolean |
impute()
Returns the impute parameter.
|
boolean |
lowmem()
Returns the lowmem parameter.
|
java.io.File |
map()
Returns the map parameter.
|
float |
mapscale()
Returns the mapscale parameter.
|
float |
maxlr()
Returns the maxlr parameter.
|
float |
modelscale()
Returns the modelscale parameter.
|
float |
ne()
Returns the ne parameter
|
int |
niterations()
Returns the niterations parameter.
|
int |
nsamples()
Return the nsamples parameter.
|
int |
nthreads()
Returns the nthreads parameter.
|
java.lang.String |
out()
Returns the out parameter.
|
int |
overlap()
Return the overlap parameter.
|
java.io.File |
ped()
Returns the ped parameter or
null
if no ped parameter was specified. |
int |
phase_its()
Returns the phase-its parameter.
|
java.io.File |
ref()
Returns the ref parameter or
null if no ref parameter was
specified. |
long |
seed()
Returns the seed parameter.
|
static java.lang.String |
usage()
Returns a description of the possible Beagle command line arguments.
|
int |
window()
Returns the window parameter.
|
public Par(java.lang.String[] args)
Parameters
instance from the specified
command line arguments.args
- the Beagle command line argumentsjava.lang.IllegalArgumentException
- if a command line argument
is incorrectly specifiedjava.lang.NumberFormatException
- if a numeric value for a parameter
is incorrectly specifiedpublic java.lang.String[] args()
public static java.lang.String usage()
public float adjustedIbdScale(int nSamples)
Math.max(2.0f, (float) Math.sqrt(nSamples/100.0))
if
this.ibdscale() == 0f
, and returns
this.ibdscale()
otherwise.nSamples
- the number of samplesthis.ibdscale() == 0f
, and this.ibdscale()
otherwisejava.lang.IllegalArgumentException
- if nSamples < 0
public java.io.File gt()
null
if no gt parameter was
specified.null
if no gt parameter was
specifiedpublic java.io.File gl()
null
if no gl parameter was
specified.null
if no gl parameter was
specifiedpublic java.io.File gtgl()
null
if no gtgl parameter was
specified.null
if no gtgl parameter was
specified.public java.io.File ref()
null
if no ref parameter was
specified.null
if no ref parameter was
specifiedpublic java.io.File dag()
null
if no ref parameter was
specified.null
if no ref parameter was
specifiedpublic java.lang.String out()
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 java.io.File ped()
null
if no ped parameter was specified.null
if no ped parameter was specifiedpublic java.io.File map()
public java.lang.String chrom()
null
if no chrom parameter was specified.null
if no chrom parameter was specifiedpublic float maxlr()
public int nthreads()
public boolean lowmem()
public int window()
public int overlap()
public long seed()
public int niterations()
public boolean impute()
public boolean gprobs()
public float ne()
public float err()
public float cluster()
public boolean ibd()
public float ibdlod()
public float ibdscale()
public int ibdtrim()
public float modelscale()
public int burnin_its()
public int phase_its()
public int nsamples()
public float mapscale()
public float ibdlength()
public float ibdextend()