VariantContextBuilder (htsjdk 2.8.1 API)

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

All Methods Instance Methods Concrete Methods
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)`
`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()`
`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`	`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
  - 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 -
    
    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 any existing attributes with
  - 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:
  - 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:
  - 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 -
  - filters
```
public VariantContextBuilder filters(java.lang.String... filters)
```
    filters
    
    Parameters:
    
    filters -
    
    Returns:
  - filter
```
public VariantContextBuilder filter(java.lang.String filter)
```
  - passFilters
```
public VariantContextBuilder passFilters()
```
    Tells this builder that the resulting VariantContext should have PASS filters
    
    Returns:
  - unfiltered
```
public VariantContextBuilder unfiltered()
```
    Tells this builder that the resulting VariantContext be unfiltered
    
    Returns:
  - genotypes
```
public VariantContextBuilder genotypes(GenotypesContext genotypes)
```
    Tells this builder that the resulting VariantContext should use this genotype's GenotypeContext. Note that genotypes can be null -> meaning there are no genotypes
    
    Parameters:
    
    genotypes -
  - 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 -
  - genotypes
```
public VariantContextBuilder genotypes(Genotype... genotypes)
```
    Tells this builder that the resulting VariantContext should use a GenotypeContext containing genotypes
    
    Parameters:
    
    genotypes -
  - 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 -
    
    Returns:
  - noID
```
public VariantContextBuilder noID()
```
    Tells us that the resulting VariantContext should not have an ID
    
    Returns:
  - log10PError
```
public VariantContextBuilder log10PError(double log10PError)
```
    Tells us that the resulting VariantContext should have log10PError
    
    Parameters:
    
    log10PError -
    
    Returns:
  - source
```
public VariantContextBuilder source(java.lang.String source)
```
    Tells us that the resulting VariantContext should have source field set to source
    
    Parameters:
    
    source -
    
    Returns:
  - 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 -
    
    start -
    
    stop -
    
    Returns:
  - chr
```
public VariantContextBuilder chr(java.lang.String contig)
```
    Tells us that the resulting VariantContext should have the specified contig chr
    
    Parameters:
    
    contig -
    
    Returns:
  - start
```
public VariantContextBuilder start(long start)
```
    Tells us that the resulting VariantContext should have the specified contig start
    
    Parameters:
    
    start -
    
    Returns:
  - stop
```
public VariantContextBuilder stop(long stop)
```
    Tells us that the resulting VariantContext should have the specified contig stop
    
    Parameters:
    
    stop -
    
    Returns:
  - 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)
```

Class VariantContextBuilder

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

VariantContextBuilder

VariantContextBuilder

VariantContextBuilder

VariantContextBuilder

Method Detail

copy

alleles

alleles

alleles

getAlleles

attributes

attribute

rmAttribute

rmAttributes

filters

filters

filter

passFilters

unfiltered

genotypes

genotypesNoValidation

genotypes

genotypes

noGenotypes

id

noID

log10PError

source

loc

chr

start

stop

computeEndFromAlleles

computeEndFromAlleles

isFullyDecoded

fullyDecoded

make

make