Package htsjdk.variant.variantcontext

Class VariantContextUtils

java.lang.Object
htsjdk.variant.variantcontext.VariantContextUtils
public class VariantContextUtils extends Object

  • Field Details

    • engine

      public static final Lazy<org.apache.commons.jexl2.JexlEngine> engine
      Use a Lazy JexlEngine instance to avoid class-loading issues. (Applications that access this class are otherwise forced to build a JexlEngine instance, which depends on some apache logging libraries that mightn't be packaged.)

  • Constructor Details

    • VariantContextUtils

      public VariantContextUtils()

  • Method Details

    • calculateAltAlleleFrequency

      public static double calculateAltAlleleFrequency(VariantContext vc)
      Computes the alternate allele frequency at the provided VariantContext by dividing its "AN" by its "AC".
      Parameters:
      vc - The variant whose alternate allele frequency is computed
      Returns:
      The alternate allele frequency in [0, 1]
      Throws:
      AssertionError - When either annotation is missing, or when the compuated frequency is outside the expected range

    • calculateChromosomeCounts

      public static Map<String,Object> calculateChromosomeCounts(VariantContext vc, Map<String,Object> attributes, boolean removeStaleValues)
      Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
      Parameters:
      vc - the VariantContext
      attributes - the attributes map to populate; must not be null; may contain old values
      removeStaleValues - should we remove stale values from the mapping?
      Returns:
      the attributes map provided as input, returned for programming convenience

    • calculateChromosomeCounts

      public static Map<String,Object> calculateChromosomeCounts(VariantContext vc, Map<String,Object> attributes, boolean removeStaleValues, Set<String> founderIds)
      Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
      Parameters:
      vc - the VariantContext
      attributes - the attributes map to populate; must not be null; may contain old values
      removeStaleValues - should we remove stale values from the mapping?
      founderIds - - Set of founders Ids to take into account. AF and FC will be calculated over the founders. If empty or null, counts are generated for all samples as unrelated individuals
      Returns:
      the attributes map provided as input, returned for programming convenience

    • calculateChromosomeCounts

      public static void calculateChromosomeCounts(VariantContextBuilder builder, boolean removeStaleValues)
      Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper chromosome-based VCF tags based on the current VC produced by builder.make()
      Parameters:
      builder - the VariantContextBuilder we are updating
      removeStaleValues - should we remove stale values from the mapping?

    • calculateChromosomeCounts

      public static void calculateChromosomeCounts(VariantContextBuilder builder, boolean removeStaleValues, Set<String> founderIds)
      Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper chromosome-based VCF tags based on the current VC produced by builder.make()
      Parameters:
      builder - the VariantContextBuilder we are updating
      founderIds - - Set of founders to take into account. AF and FC will be calculated over the founders only. If empty or null, counts are generated for all samples as unrelated individuals
      removeStaleValues - should we remove stale values from the mapping?

    • getMetaDataForField

      public static final VCFCompoundHeaderLine getMetaDataForField(VCFHeader header, String field)

    • initializeMatchExps

      public static List<VariantContextUtils.JexlVCMatchExp> initializeMatchExps(String[] names, String[] exps)
      Method for creating JexlVCMatchExp from input walker arguments names and exps. These two arrays contain the name associated with each JEXL expression. initializeMatchExps will parse each expression and return a list of JexlVCMatchExp, in order, that correspond to the names and exps. These are suitable input to match() below.
      Parameters:
      names - names
      exps - expressions
      Returns:
      list of matches

    • initializeMatchExps

      public static List<VariantContextUtils.JexlVCMatchExp> initializeMatchExps(List<String> names, List<String> exps)
      Method for creating JexlVCMatchExp from input walker arguments names and exps. These two lists contain the name associated with each JEXL expression. initializeMatchExps will parse each expression and return a list of JexlVCMatchExp, in order, that correspond to the names and exps. These are suitable input to match() below.
      Parameters:
      names - names
      exps - expressions
      Returns:
      list of matches

    • initializeMatchExps

      public static List<VariantContextUtils.JexlVCMatchExp> initializeMatchExps(Map<String,String> names_and_exps)
      Method for creating JexlVCMatchExp from input walker arguments mapping from names to exps. These two arrays contain the name associated with each JEXL expression. initializeMatchExps will parse each expression and return a list of JexlVCMatchExp, in order, that correspond to the names and exps. These are suitable input to match() below.
      Parameters:
      names_and_exps - mapping of names to expressions
      Returns:
      list of matches

    • match

      public static boolean match(VariantContext vc, VariantContextUtils.JexlVCMatchExp exp)
      Returns true if exp match vc. See match(VariantContext, Collection) for full docs.
      Parameters:
      vc - variant context
      exp - expression
      Returns:
      true if there is a match

    • match

      public static Map<VariantContextUtils.JexlVCMatchExp,Boolean> match(VariantContext vc, Collection<VariantContextUtils.JexlVCMatchExp> exps)
      Matches each VariantContextUtils.JexlVCMatchExp exp against the data contained in vc, and returns a map from these expressions to true (if they matched) or false (if they didn't). This the best way to apply JEXL expressions to VariantContext records. Use the various initializeMatchExps()'s to create the list of VariantContextUtils.JexlVCMatchExp expressions. Expressions that contain literals not available in the VariantContext or Genotype will be treated as not matching
      Parameters:
      vc - variant context
      exps - expressions
      Returns:
      true if there is a match

    • match

      public static boolean match(VariantContext vc, Genotype g, VariantContextUtils.JexlVCMatchExp exp)
      Returns true if exp match vc, g. See match(VariantContext, Genotype, Collection) for full docs.
      Parameters:
      vc - variant context
      g - genotype
      exp - expression
      Returns:
      true if there is a match

    • match

      public static boolean match(VariantContext vc, Genotype g, VariantContextUtils.JexlVCMatchExp exp, JexlMissingValueTreatment howToTreatMissingValues)
      Returns true if exp match vc, g. See match(VariantContext, Genotype, Collection) for full docs.
      Parameters:
      vc - variant context
      g - genotype
      exp - expression
      howToTreatMissingValues - what to do if the jexl expression contains literals that aren't in the context
      Returns:
      true if there is a match

    • match

      public static Map<VariantContextUtils.JexlVCMatchExp,Boolean> match(VariantContext vc, Genotype g, Collection<VariantContextUtils.JexlVCMatchExp> exps)
      Matches each VariantContextUtils.JexlVCMatchExp exp against the data contained in vc, g, and returns a map from these expressions to true (if they matched) or false (if they didn't). This the best way to apply JEXL expressions to VariantContext records. Use the various initializeMatchExps()'s to create the list of VariantContextUtils.JexlVCMatchExp expressions. Expressions that contain literals not available in the VariantContext or Genotype will be treated as not matching
      Parameters:
      vc - variant context
      g - genotype
      exps - expressions
      Returns:
      true if there is a match

    • match

      public static Map<VariantContextUtils.JexlVCMatchExp,Boolean> match(VariantContext vc, Genotype g, Collection<VariantContextUtils.JexlVCMatchExp> exps, JexlMissingValueTreatment howToTreatMissingValues)
      Matches each VariantContextUtils.JexlVCMatchExp exp against the data contained in vc, g, and returns a map from these expressions to true (if they matched) or false (if they didn't). This the best way to apply JEXL expressions to VariantContext records. Use the various initializeMatchExps()'s to create the list of VariantContextUtils.JexlVCMatchExp expressions.
      Parameters:
      vc - variant context
      g - genotype
      exps - expressions
      howToTreatMissingValues - what to do if the jexl expression contains literals that aren't in the context
      Returns:
      true if there is a match

    • isTransition

      public static boolean isTransition(VariantContext vc) throws IllegalArgumentException
      Answers if the provided variant is transitional (otherwise, it's transversional). Transitions: A->G G->A C->T T->C

      Transversions: A->C A->T C->A C->G G->C G->T T->A T->G

      Parameters:
      vc - a biallelic polymorphic SNP
      Returns:
      true if a transition and false if transversion
      Throws:
      IllegalArgumentException - if vc is monomorphic, not a SNP or not bi-allelic.

    • sitesOnlyVariantContext

      public static VariantContext sitesOnlyVariantContext(VariantContext vc)
      Returns a newly allocated VC that is the same as VC, but without genotypes
      Parameters:
      vc - variant context
      Returns:
      new VC without genotypes

    • sitesOnlyVariantContexts

      public static Collection<VariantContext> sitesOnlyVariantContexts(Collection<VariantContext> vcs)
      Returns a newly allocated list of VC, where each VC is the same as the input VCs, but without genotypes
      Parameters:
      vcs - collection of VCs
      Returns:
      new VCs without genotypes

    • getSize

      public static int getSize(VariantContext vc)

    • genotypeNames

      public static Set<String> genotypeNames(Collection<Genotype> genotypes)

    • computeEndFromAlleles

      public static int computeEndFromAlleles(List<Allele> alleles, int start, int endForSymbolicAlleles)
      Compute the end position for this VariantContext from the alleles themselves In the trivial case this is a single BP event and end = start (open intervals) In general the end is start + ref length - 1, handling the case where ref length == 0 However, if alleles contains a symbolic allele then we use endForSymbolicAllele in all cases
      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