htsjdk.variant.variantcontext

Class VariantContextBuilder

java.lang.Object

htsjdk.variant.variantcontext.VariantContextBuilder

public class VariantContextBuilder
extends java.lang.Object

Builder class for VariantContext.

Some basic assumptions here:

1. data isn't protectively copied. If you provide an attribute map to the build, and modify it later, the builder will see this and so will any resulting variant contexts. It's best not to modify collections provided to a builder.
2. the system uses the standard builder model, allowing the simple construction idiom:

   builder.source("a").genotypes(gc).id("x").make() => VariantContext

3. The best way to copy a VariantContext is:

   new VariantContextBuilder(vc).make() => a copy of VC

4. validation of arguments is done at the during the final make() call, so a VariantContextBuilder can exist in an inconsistent state as long as those issues are resolved before the call to make() is issued.

Constructor Summary

Constructors

Constructor and Description
VariantContextBuilder() Create an empty VariantContextBuilder where all values adopt their default values.
VariantContextBuilder(java.lang.String source, java.lang.String contig, long start, long stop, java.util.Collection<Allele> alleles) Create an empty VariantContextBuilder where all values adopt their default values, but the bare min.
VariantContextBuilder(VariantContext parent) Returns a new builder based on parent -- the new VC will have all fields initialized to their corresponding values in parent.
VariantContextBuilder(VariantContextBuilder parent)

Method Summary

Modifier and Type	Method and Description
VariantContextBuilder	alleles(java.util.Collection<Allele> alleles) Tells this builder to use this collection of alleles for the resulting VariantContext
VariantContextBuilder	alleles(java.util.List<java.lang.String> alleleStrings)
VariantContextBuilder	alleles(java.lang.String... alleleStrings)
VariantContextBuilder	attribute(java.lang.String key, java.lang.Object value) Puts the key -> value mapping into this builder's attributes
VariantContextBuilder	attributes(java.util.Map<java.lang.String,?> attributes) Tells this builder to use this map of attributes for the resulting VariantContext.
VariantContextBuilder	chr(java.lang.String contig) Tells us that the resulting VariantContext should have the specified contig chr
VariantContextBuilder	computeEndFromAlleles(java.util.List<Allele> alleles, int start)
VariantContextBuilder	computeEndFromAlleles(java.util.List<Allele> alleles, int start, int endForSymbolicAlleles) Compute the end position for this VariantContext from the alleles themselves assigns this builder the stop position computed.
VariantContextBuilder	copy()
VariantContextBuilder	filter(java.lang.String filter) Adds the given filter to the list of filters
VariantContextBuilder	filters(java.util.Set<java.lang.String> filters) This builder's filters are set to this value filters can be null -> meaning there are no filters
VariantContextBuilder	filters(java.lang.String... filters) filters
VariantContextBuilder	fullyDecoded(boolean isFullyDecoded) Sets this builder's fully decoded state to true.
VariantContextBuilder	genotypes(java.util.Collection<Genotype> genotypes) Tells this builder that the resulting VariantContext should use a GenotypeContext containing genotypes Note that genotypes can be null, meaning there are no genotypes
VariantContextBuilder	genotypes(Genotype... genotypes) Tells this builder that the resulting VariantContext should use a GenotypeContext containing genotypes
VariantContextBuilder	genotypes(GenotypesContext genotypes) Tells this builder that the resulting VariantContext should use this genotype's GenotypeContext.
VariantContextBuilder	genotypesNoValidation(GenotypesContext genotypes)
java.util.List<Allele>	getAlleles()
java.util.Map<java.lang.String,java.lang.Object>	getAttributes() Getter for attributes (DANGEROUS!!! DOES NOT MAKE A COPY!!!)
java.lang.String	getContig() Getter for contig
java.util.Set<java.lang.String>	getFilters() Getter for filters (DANGEROUS!!! DOES NOT MAKE A COPY!!!)
GenotypesContext	getGenotypes() Getter for genotypes (DANGEROUS!!! DOES NOT MAKE A COPY!!!)
java.lang.String	getID() Getter for id of variant
long	getStart() Getter for start position
long	getStop() Getter for stop position
VariantContextBuilder	id(java.lang.String ID) Tells us that the resulting VariantContext should have ID
boolean	isFullyDecoded()
VariantContextBuilder	loc(java.lang.String contig, long start, long stop) Tells us that the resulting VariantContext should have the specified location
VariantContextBuilder	log10PError(double log10PError) Tells us that the resulting VariantContext should have log10PError
VariantContext	make() Takes all of the builder data provided up to this point, and instantiates a freshly allocated VariantContext with all of the builder data.
VariantContext	make(boolean leaveModifyableAsIs)
VariantContextBuilder	noGenotypes() Tells this builder that the resulting VariantContext should not contain any GenotypeContext
VariantContextBuilder	noID() Tells us that the resulting VariantContext should not have an ID
VariantContextBuilder	passFilters() Tells this builder that the resulting VariantContext should have PASS filters
VariantContextBuilder	putAttributes(java.util.Map<java.lang.String,?> attributes) Tells this builder to put this map of attributes into the resulting VariantContext.
VariantContextBuilder	rmAttribute(java.lang.String key) Removes key if present in the attributes
VariantContextBuilder	rmAttributes(java.util.List<java.lang.String> keys) Removes list of keys if present in the attributes
VariantContextBuilder	source(java.lang.String source) Tells us that the resulting VariantContext should have source field set to source
VariantContextBuilder	start(long start) Tells us that the resulting VariantContext should have the specified contig start
VariantContextBuilder	stop(long stop) Tells us that the resulting VariantContext should have the specified contig stop
VariantContextBuilder	unfiltered() Tells this builder that the resulting VariantContext be unfiltered

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantContextBuilder

public VariantContextBuilder()

Create an empty VariantContextBuilder where all values adopt their default values. Note that source, chr, start, stop, and alleles must eventually be filled in, or the resulting VariantContext will throw an error.

VariantContextBuilder

public VariantContextBuilder(java.lang.String source,
                             java.lang.String contig,
                             long start,
                             long stop,
                             java.util.Collection<Allele> alleles)

Create an empty VariantContextBuilder where all values adopt their default values, but the bare min. of info (source, chr, start, stop, and alleles) have been provided to start.

VariantContextBuilder

public VariantContextBuilder(VariantContext parent)

Returns a new builder based on parent -- the new VC will have all fields initialized to their corresponding values in parent. This is the best way to create a derived VariantContext

Parameters:

parent - Cannot be null

VariantContextBuilder

public VariantContextBuilder(VariantContextBuilder parent)

Method Detail

getContig

public java.lang.String getContig()

Getter for contig

Returns:

the current contig

getStart

public long getStart()

Getter for start position

Returns:

the current start position

getStop

public long getStop()

Getter for stop position

Returns:

the current stop position

getID

public java.lang.String getID()

Getter for id of variant

Returns:

the current variant id

getGenotypes

public GenotypesContext getGenotypes()

Getter for genotypes (DANGEROUS!!! DOES NOT MAKE A COPY!!!)

Returns:

the current GenotypeContext

getFilters

public java.util.Set<java.lang.String> getFilters()

Getter for filters (DANGEROUS!!! DOES NOT MAKE A COPY!!!)

Returns:

the current set of filters

getAttributes

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

Getter for attributes (DANGEROUS!!! DOES NOT MAKE A COPY!!!)

Returns:

the current map of attributes

copy

public VariantContextBuilder copy()

alleles

public VariantContextBuilder alleles(java.util.Collection<Allele> alleles)

Tells this builder to use this collection of alleles for the resulting VariantContext

Parameters:

alleles - a Collection of alleles to set as the alleles of this builder

Returns:

this builder

alleles

public VariantContextBuilder alleles(java.util.List<java.lang.String> alleleStrings)

alleles

public VariantContextBuilder alleles(java.lang.String... alleleStrings)

getAlleles

public java.util.List<Allele> getAlleles()

attributes

public VariantContextBuilder attributes(java.util.Map<java.lang.String,?> attributes)

Tells this builder to use this map of attributes for the resulting VariantContext. The contents of the Map are copied to a new Map to ensure that modifications to the provided Map post-invocation don't affect the VariantContext and also to ensure additional attributes can be added in case the provided map doesn't support changes (e.g. UnmodifiableMap). Attributes can be null -> meaning there are no attributes. After calling this routine the builder assumes it can modify the attributes object here, if subsequent calls are made to set attribute values Value for each attribute must be of a type that implements Serializable or else serialization will fail.

Parameters:

attributes - a Map of attributes to replace existing attributes with

putAttributes

public VariantContextBuilder putAttributes(java.util.Map<java.lang.String,?> attributes)

Tells this builder to put this map of attributes into the resulting VariantContext. The contents of the Map are copied to the current Map (or a new one is created if null) After calling this routine the builder assumes it can modify the attributes object here, if subsequent calls are made to set attribute values Value for each attribute must be of a type that implements Serializable or else serialization will fail.

Parameters:

attributes - a Map of attributes to complement any existing attributes with, overwriting any that share the same key.

attribute

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

Puts the key -> value mapping into this builder's attributes

Parameters:

key - key for the attribute

value - value for the attribute (must be of a type that implements Serializable or else serialization will fail)

rmAttribute

public VariantContextBuilder rmAttribute(java.lang.String key)

Removes key if present in the attributes

Parameters:

key - key to remove

Returns:

this builder

rmAttributes

public VariantContextBuilder rmAttributes(java.util.List<java.lang.String> keys)

Removes list of keys if present in the attributes

Parameters:

keys - list of keys to remove

Returns:

this builder

filters

public VariantContextBuilder filters(java.util.Set<java.lang.String> filters)

This builder's filters are set to this value filters can be null -> meaning there are no filters

Parameters:

filters - Set of strings to set as the filters for this builder This set will be copied so that external set can be safely changed.

Returns:

this builder

filters

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

filters

Parameters:

filters - Strings to set as the filters for this builder

Returns:

this builder

filter

public VariantContextBuilder filter(java.lang.String filter)

Adds the given filter to the list of filters

Parameters:

filter -

Returns:

passFilters

public VariantContextBuilder passFilters()

Tells this builder that the resulting VariantContext should have PASS filters

Returns:

this builder

unfiltered

public VariantContextBuilder unfiltered()

Tells this builder that the resulting VariantContext be unfiltered

Returns:

this builder

genotypes

public VariantContextBuilder genotypes(GenotypesContext genotypes)

Tells this builder that the resulting VariantContext should use this genotype's GenotypeContext. Note that this method will call the immutable method on the provided genotypes object to ensure that the user will not modify it further. Note that genotypes can be null -> meaning there are no genotypes

Parameters:

genotypes - GenotypeContext to use in this builder

Returns:

this builder

genotypesNoValidation

public VariantContextBuilder genotypesNoValidation(GenotypesContext genotypes)

genotypes

public VariantContextBuilder genotypes(java.util.Collection<Genotype> genotypes)

Tells this builder that the resulting VariantContext should use a GenotypeContext containing genotypes Note that genotypes can be null, meaning there are no genotypes

Parameters:

genotypes - Collection of genotypes to set as genotypes for this builder

genotypes

public VariantContextBuilder genotypes(Genotype... genotypes)

Tells this builder that the resulting VariantContext should use a GenotypeContext containing genotypes

Parameters:

genotypes - genotypes to set as genotypes for this builder

noGenotypes

public VariantContextBuilder noGenotypes()

Tells this builder that the resulting VariantContext should not contain any GenotypeContext

id

public VariantContextBuilder id(java.lang.String ID)

Tells us that the resulting VariantContext should have ID

Parameters:

ID - id of variant

Returns:

this builder

noID

public VariantContextBuilder noID()

Tells us that the resulting VariantContext should not have an ID

Returns:

this builder

log10PError

public VariantContextBuilder log10PError(double log10PError)

Tells us that the resulting VariantContext should have log10PError

Parameters:

log10PError - value of QUAL field for this builder

Returns:

this builder

source

public VariantContextBuilder source(java.lang.String source)

Tells us that the resulting VariantContext should have source field set to source

Parameters:

source - string describing the source of the variant

Returns:

this builder

loc

public VariantContextBuilder loc(java.lang.String contig,
                                 long start,
                                 long stop)

Tells us that the resulting VariantContext should have the specified location

Parameters:

contig - the contig the variant is on (must be in the dictionary)

start - the start position of the variant

stop - the end position of the variant

Returns:

this builder

chr

public VariantContextBuilder chr(java.lang.String contig)

Tells us that the resulting VariantContext should have the specified contig chr

Parameters:

contig - the contig of the variant

Returns:

this builder

start

public VariantContextBuilder start(long start)

Tells us that the resulting VariantContext should have the specified contig start

Parameters:

start - the start position of the variant

Returns:

this builder

stop

public VariantContextBuilder stop(long stop)

Tells us that the resulting VariantContext should have the specified contig stop

Parameters:

stop - the stop position of the variant

Returns:

this builder

computeEndFromAlleles

public VariantContextBuilder computeEndFromAlleles(java.util.List<Allele> alleles,
                                                   int start)

See Also:

with endForSymbolicAlleles == -1

computeEndFromAlleles

public VariantContextBuilder computeEndFromAlleles(java.util.List<Allele> alleles,
                                                   int start,
                                                   int endForSymbolicAlleles)

Compute the end position for this VariantContext from the alleles themselves assigns this builder the stop position computed.

Parameters:

alleles - the list of alleles to consider. The reference allele must be the first one

start - the known start position of this event

endForSymbolicAlleles - the end position to use if any of the alleles is symbolic. Can be -1 if no is expected but will throw an error if one is found

Returns:

this builder

isFullyDecoded

public boolean isFullyDecoded()

Returns:

true if this builder contains fully decoded data See VariantContext for more information

fullyDecoded

public VariantContextBuilder fullyDecoded(boolean isFullyDecoded)

Sets this builder's fully decoded state to true. A fully decoded builder indicates that all fields are represented by their proper java objects (e.g., Integer(10) not "10"). See VariantContext for more information

Parameters:

isFullyDecoded -

make

public VariantContext make()

Takes all of the builder data provided up to this point, and instantiates a freshly allocated VariantContext with all of the builder data. This VariantContext is validated as appropriate and if not failing QC (and throwing an exception) is returned. Note that this function can be called multiple times to create multiple VariantContexts from the same builder.

make

public VariantContext make(boolean leaveModifyableAsIs)