Class 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 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​(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
    • Method Detail

      • 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
      • 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
      • 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)
        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
      • 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,
                                                           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.