Field Detail

• 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 Detail

• VariantContextUtils

  public VariantContextUtils()

Method Detail

• 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