Package htsjdk.variant.variantcontext

Class GenotypeBuilder

java.lang.Object
htsjdk.variant.variantcontext.GenotypeBuilder
public final class GenotypeBuilder extends 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 Details

    • 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(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(String sampleName, 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 Details

    • create

      public static Genotype create(String sampleName, List<Allele> alleles)

    • create

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

    • create

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

    • createMissing

      public static Genotype createMissing(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(String sampleName)
      Set this genotype's name
      Parameters:
      sampleName -
      Returns:

    • alleles

      public GenotypeBuilder alleles(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(Map<String,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(String key, 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(List<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(String... filters)
      varargs version of #filters
      Parameters:
      filters -
      Returns:

    • filter

      public GenotypeBuilder filter(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: