htsjdk.variant.variantcontext

Class VariantContextUtils

java.lang.Object

htsjdk.variant.variantcontext.VariantContextUtils

public class VariantContextUtils
extends java.lang.Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	VariantContextUtils.JexlVCMatchExp A simple but common wrapper for matching VariantContext objects using JEXL expressions

Field Summary

Fields

Modifier and Type	Field and Description
static Lazy<org.apache.commons.jexl2.JexlEngine>	engine Use a Lazy JexlEngine instance to avoid class-loading issues.

Constructor Summary

Constructors

Constructor and Description
VariantContextUtils()

Method Summary

Methods

Modifier and Type	Method and Description
static double	calculateAltAlleleFrequency(VariantContext vc) Computes the alternate allele frequency at the provided VariantContext by dividing its "AN" by its "AC".
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()
static void	calculateChromosomeCounts(VariantContextBuilder builder, boolean removeStaleValues, java.util.Set<java.lang.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()
static java.util.Map<java.lang.String,java.lang.Object>	calculateChromosomeCounts(VariantContext vc, java.util.Map<java.lang.String,java.lang.Object> attributes, boolean removeStaleValues) Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
static java.util.Map<java.lang.String,java.lang.Object>	calculateChromosomeCounts(VariantContext vc, java.util.Map<java.lang.String,java.lang.Object> attributes, boolean removeStaleValues, java.util.Set<java.lang.String> founderIds) Update the attributes of the attributes map given the VariantContext to reflect the proper chromosome-based VCF tags
static int	computeEndFromAlleles(java.util.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
static java.util.Set<java.lang.String>	genotypeNames(java.util.Collection<Genotype> genotypes)
static VCFCompoundHeaderLine	getMetaDataForField(VCFHeader header, java.lang.String field)
static int	getSize(VariantContext vc)
static java.util.List<VariantContextUtils.JexlVCMatchExp>	initializeMatchExps(java.util.ArrayList<java.lang.String> names, java.util.ArrayList<java.lang.String> exps)
static java.util.List<VariantContextUtils.JexlVCMatchExp>	initializeMatchExps(java.util.Map<java.lang.String,java.lang.String> names_and_exps) Method for creating JexlVCMatchExp from input walker arguments mapping from names to exps.
static java.util.List<VariantContextUtils.JexlVCMatchExp>	initializeMatchExps(java.lang.String[] names, java.lang.String[] exps) Method for creating JexlVCMatchExp from input walker arguments names and exps.
static java.util.Map<VariantContextUtils.JexlVCMatchExp,java.lang.Boolean>	match(VariantContext vc, java.util.Collection<VariantContextUtils.JexlVCMatchExp> exps) Matches each 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).
static java.util.Map<VariantContextUtils.JexlVCMatchExp,java.lang.Boolean>	match(VariantContext vc, Genotype g, java.util.Collection<VariantContextUtils.JexlVCMatchExp> exps) Matches each 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).
static boolean	match(VariantContext vc, Genotype g, VariantContextUtils.JexlVCMatchExp exp) Returns true if exp match VC/g.
static boolean	match(VariantContext vc, VariantContextUtils.JexlVCMatchExp exp) Returns true if exp match VC.
static VariantContext	sitesOnlyVariantContext(VariantContext vc) Returns a newly allocated VC that is the same as VC, but without genotypes
static java.util.Collection<VariantContext>	sitesOnlyVariantContexts(java.util.Collection<VariantContext> vcs) Returns a newly allocated list of VC, where each VC is the same as the input VCs, but without genotypes

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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:

java.lang.AssertionError - When either annotation is missing, or when the compuated frequency is outside the expected range

calculateChromosomeCounts

public static java.util.Map<java.lang.String,java.lang.Object> calculateChromosomeCounts(VariantContext vc,
                                                                         java.util.Map<java.lang.String,java.lang.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 java.util.Map<java.lang.String,java.lang.Object> calculateChromosomeCounts(VariantContext vc,
                                                                         java.util.Map<java.lang.String,java.lang.Object> attributes,
                                                                         boolean removeStaleValues,
                                                                         java.util.Set<java.lang.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,
                             java.util.Set<java.lang.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,
                                        java.lang.String field)

initializeMatchExps

public static java.util.List<VariantContextUtils.JexlVCMatchExp> initializeMatchExps(java.lang.String[] names,
                                                                     java.lang.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 java.util.List<VariantContextUtils.JexlVCMatchExp> initializeMatchExps(java.util.ArrayList<java.lang.String> names,
                                                                     java.util.ArrayList<java.lang.String> exps)

initializeMatchExps

public static java.util.List<VariantContextUtils.JexlVCMatchExp> initializeMatchExps(java.util.Map<java.lang.String,java.lang.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 java.util.Map<VariantContextUtils.JexlVCMatchExp,java.lang.Boolean> match(VariantContext vc,
                                                                        java.util.Collection<VariantContextUtils.JexlVCMatchExp> exps)

Matches each 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 initializeMatchExps() to create the list of JexlVCMatchExp expressions.

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, Collection) for full docs.

Parameters:

vc - variant context

g - genotype

exp - expression

Returns:

true if there is a match

match

public static java.util.Map<VariantContextUtils.JexlVCMatchExp,java.lang.Boolean> match(VariantContext vc,
                                                                        Genotype g,
                                                                        java.util.Collection<VariantContextUtils.JexlVCMatchExp> exps)

Matches each 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/genotypes. Use initializeMatchExps() to create the list of JexlVCMatchExp expressions.

Parameters:

vc - variant context

g - genotype

exps - expressions

Returns:

true if there is a match

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 java.util.Collection<VariantContext> sitesOnlyVariantContexts(java.util.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 java.util.Set<java.lang.String> genotypeNames(java.util.Collection<Genotype> genotypes)

computeEndFromAlleles

public static int computeEndFromAlleles(java.util.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