htsjdk.variant.variantcontext

Class GenotypeBuilder

java.lang.Object

htsjdk.variant.variantcontext.GenotypeBuilder

public final class GenotypeBuilder
extends java.lang.Object

A builder class for genotypes Provides convenience setter methods for all of the Genotype field values. Setter methods can be used in any order, allowing you to pass through states that wouldn't be allowed in the highly regulated immutable Genotype class. All fields default to meaningful MISSING values. Call make() to actually create the corresponding Genotype object from this builder. Can be called multiple times to create independent copies, or with intervening sets to conveniently make similar Genotypes with slight modifications. Re-using the same GenotypeBuilder to build multiple Genotype objects via calls to make() is dangerous, since reference types in the builder (eg., Collections/arrays) don't get copied when making each Genotype. To safely re-use the same builder object multiple times, use makeWithShallowCopy() instead of make().

Since:

06/12

Constructor Summary

Constructors

Constructor and Description
GenotypeBuilder() Create a empty builder.
GenotypeBuilder(Genotype g) Create a new builder starting with the values in Genotype g
GenotypeBuilder(java.lang.String sampleName) Create a builder using sampleName.
GenotypeBuilder(java.lang.String sampleName, java.util.List<Allele> alleles) Make a builder using sampleName and alleles for starting values

Method Summary

Modifier and Type	Method and Description
GenotypeBuilder	AD(int[] AD) This genotype has this AD value
GenotypeBuilder	alleles(java.util.List<Allele> alleles) Set this genotype's alleles
GenotypeBuilder	attribute(java.lang.String key, java.lang.Object value) This genotype has this attribute key / value pair.
GenotypeBuilder	attributes(java.util.Map<java.lang.String,java.lang.Object> attributes) This genotype has these attributes.
GenotypeBuilder	copy(Genotype g) Copy all of the values for this builder from Genotype g
static Genotype	create(java.lang.String sampleName, java.util.List<Allele> alleles)
protected static Genotype	create(java.lang.String sampleName, java.util.List<Allele> alleles, double[] gls)
static Genotype	create(java.lang.String sampleName, java.util.List<Allele> alleles, java.util.Map<java.lang.String,java.lang.Object> attributes)
static Genotype	createMissing(java.lang.String sampleName, int ploidy) Create a new Genotype object for a sample that's missing from the VC (i.e., in the output header).
GenotypeBuilder	DP(int DP) This genotype has this DP value
GenotypeBuilder	filter(java.lang.String filter) Most efficient version of setting filters -- just set the filters string to filters
GenotypeBuilder	filters(java.util.List<java.lang.String> filters) Tells this builder to make a Genotype object that has had filters applied, which may be empty (passes) or have some value indicating the reasons why it's been filtered.
GenotypeBuilder	filters(java.lang.String... filters) varargs version of #filters
GenotypeBuilder	GQ(int GQ)
GenotypeBuilder	log10PError(double pLog10Error) Set the GQ with a log10PError value
Genotype	make() Create a new Genotype object using the values set in this builder.
Genotype	makeWithShallowCopy() Create a new Genotype object using the values set in this builder, and perform a shallow copy of reference types to allow safer re-use of this builder After creation the values in this builder can be modified and more Genotypes created.
GenotypeBuilder	maxAttributes(int i) Tell's this builder that we have at most these number of attributes
GenotypeBuilder	name(java.lang.String sampleName) Set this genotype's name
GenotypeBuilder	noAD() This genotype has no AD value
GenotypeBuilder	noAttributes() Tells this builder to remove all extended attributes
GenotypeBuilder	noDP() This genotype has no DP value
GenotypeBuilder	noGQ() This genotype has no GQ value
GenotypeBuilder	noPL() This genotype has no PL value
GenotypeBuilder	phased(boolean phased) Is this genotype phased?
GenotypeBuilder	PL(double[] GLs) This genotype has this PL value, converted from double[].
GenotypeBuilder	PL(int[] PL) This genotype has this PL value, as int[].
void	reset(boolean keepSampleName) Reset all of the builder attributes to their defaults.
GenotypeBuilder	unfiltered() This genotype is unfiltered

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GenotypeBuilder

public GenotypeBuilder()

Create a empty builder. Both a sampleName and alleles must be provided before trying to make a Genotype from this builder.

GenotypeBuilder

public GenotypeBuilder(java.lang.String sampleName)

Create a builder using sampleName. Alleles must be provided before trying to make a Genotype from this builder.

Parameters:

sampleName -

GenotypeBuilder

public GenotypeBuilder(java.lang.String sampleName,
                       java.util.List<Allele> alleles)

Make a builder using sampleName and alleles for starting values

Parameters:

sampleName -

alleles -

GenotypeBuilder

public GenotypeBuilder(Genotype g)

Create a new builder starting with the values in Genotype g

Parameters:

g -

Method Detail

create

public static Genotype create(java.lang.String sampleName,
                              java.util.List<Allele> alleles)

create

public static Genotype create(java.lang.String sampleName,
                              java.util.List<Allele> alleles,
                              java.util.Map<java.lang.String,java.lang.Object> attributes)

create

protected static Genotype create(java.lang.String sampleName,
                                 java.util.List<Allele> alleles,
                                 double[] gls)

createMissing

public static Genotype createMissing(java.lang.String sampleName,
                                     int ploidy)

Create a new Genotype object for a sample that's missing from the VC (i.e., in the output header). Defaults to a diploid no call genotype ./.

Parameters:

sampleName - the name of this sample

Returns:

an initialized Genotype with sampleName that's a diploid ./. no call genotype

copy

public GenotypeBuilder copy(Genotype g)

Copy all of the values for this builder from Genotype g

Parameters:

g -

Returns:

reset

public final void reset(boolean keepSampleName)

Reset all of the builder attributes to their defaults. After this function you must provide sampleName and alleles before trying to make more Genotypes.

make

public Genotype make()

Create a new Genotype object using the values set in this builder. After creation the values in this builder can be modified and more Genotypes created, althrough the contents of array values like PL should never be modified inline as they are not copied for efficiency reasons. Note: if attributes are added via this builder after a call to make(), the new Genotype will be modified. Use makeWithShallowCopy() to safely re-use the same builder object multiple times.

Returns:

a newly minted Genotype object with values provided from this builder

makeWithShallowCopy

public Genotype makeWithShallowCopy()

Create a new Genotype object using the values set in this builder, and perform a shallow copy of reference types to allow safer re-use of this builder After creation the values in this builder can be modified and more Genotypes created.

Returns:

a newly minted Genotype object with values provided from this builder

name

public GenotypeBuilder name(java.lang.String sampleName)

Set this genotype's name

Parameters:

sampleName -

Returns:

alleles

public GenotypeBuilder alleles(java.util.List<Allele> alleles)

Set this genotype's alleles

Parameters:

alleles -

Returns:

phased

public GenotypeBuilder phased(boolean phased)

Is this genotype phased?

Parameters:

phased -

Returns:

GQ

public GenotypeBuilder GQ(int GQ)

log10PError

public GenotypeBuilder log10PError(double pLog10Error)

Set the GQ with a log10PError value

Parameters:

pLog10Error -

Returns:

noGQ

public GenotypeBuilder noGQ()

This genotype has no GQ value

Returns:

noAD

public GenotypeBuilder noAD()

This genotype has no AD value

Returns:

noDP

public GenotypeBuilder noDP()

This genotype has no DP value

Returns:

noPL

public GenotypeBuilder noPL()

This genotype has no PL value

Returns:

DP

public GenotypeBuilder DP(int DP)

This genotype has this DP value

Returns:

AD

public GenotypeBuilder AD(int[] AD)

This genotype has this AD value

Returns:

PL

public GenotypeBuilder PL(int[] PL)

This genotype has this PL value, as int[]. FAST

Returns:

PL

public GenotypeBuilder PL(double[] GLs)

This genotype has this PL value, converted from double[]. SLOW

Returns:

attributes

public GenotypeBuilder attributes(java.util.Map<java.lang.String,java.lang.Object> attributes)

This genotype has these attributes. Attributes are added to previous ones. Cannot contain inline attributes (DP, AD, GQ, PL). Note: this is not checked

Returns:

noAttributes

public GenotypeBuilder noAttributes()

Tells this builder to remove all extended attributes

Returns:

attribute

public GenotypeBuilder attribute(java.lang.String key,
                                 java.lang.Object value)

This genotype has this attribute key / value pair. Cannot contain inline attributes (DP, AD, GQ, PL). Note: this is not checked

Returns:

filters

public GenotypeBuilder filters(java.util.List<java.lang.String> filters)

Tells this builder to make a Genotype object that has had filters applied, which may be empty (passes) or have some value indicating the reasons why it's been filtered.

Parameters:

filters - non-null list of filters. empty list => PASS

Returns:

this builder

filters

public GenotypeBuilder filters(java.lang.String... filters)

varargs version of #filters

Parameters:

filters -

Returns:

filter

public GenotypeBuilder filter(java.lang.String filter)

Most efficient version of setting filters -- just set the filters string to filters

Parameters:

filter - if filters == null or filters.equals("PASS") => genotype is PASS

Returns:

unfiltered

public GenotypeBuilder unfiltered()

This genotype is unfiltered

Returns:

maxAttributes

public GenotypeBuilder maxAttributes(int i)

Tell's this builder that we have at most these number of attributes

Returns: