Package htsjdk.variant.variantcontext

Class VariantContextBuilder

java.lang.Object
htsjdk.variant.variantcontext.VariantContextBuilder
public class VariantContextBuilder extends 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 Details

    • 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(String source, String contig, long start, long stop, 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 Details

    • getContig

      public 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 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 Set<String> getFilters()
      Getter for filters (DANGEROUS!!! DOES NOT MAKE A COPY!!!)
      Returns:
      the current set of filters

    • getAttributes

      public Map<String,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(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(List<String> alleleStrings)

    • alleles

      public VariantContextBuilder alleles(String... alleleStrings)

    • getAlleles

      public List<Allele> getAlleles()

    • attributes

      public VariantContextBuilder attributes(Map<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(Map<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(String key, 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(String key)
      Removes key if present in the attributes
      Parameters:
      key - key to remove
      Returns:
      this builder

    • rmAttributes

      public VariantContextBuilder rmAttributes(List<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(Set<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(String... filters)
      filters
      Parameters:
      filters - Strings to set as the filters for this builder
      Returns:
      this builder

    • filter

      public VariantContextBuilder filter(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(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(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(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(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(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(List<Allele> alleles, int start)
      See Also:

    • computeEndFromAlleles

      public VariantContextBuilder computeEndFromAlleles(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)