Package | Description |
---|---|
htsjdk.variant.bcf2 | |
htsjdk.variant.variantcontext | |
htsjdk.variant.vcf |
Modifier and Type | Method and Description |
---|---|
void |
BCF2GenotypeFieldDecoders.Decoder.decode(java.util.List<Allele> siteAlleles,
java.lang.String field,
BCF2Decoder decoder,
byte typeDescriptor,
int numElements,
GenotypeBuilder[] gbs) |
Modifier and Type | Field and Description |
---|---|
static Allele |
Allele.NO_CALL |
static Allele |
Allele.SPAN_DEL |
Modifier and Type | Field and Description |
---|---|
protected java.util.List<Allele> |
VariantContext.alleles
A set of the alleles segregating in this context
|
Modifier and Type | Method and Description |
---|---|
static Allele |
Allele.create(Allele allele,
boolean ignoreRefState)
Creates a new allele based on the provided one.
|
static Allele |
Allele.create(byte base) |
static Allele |
Allele.create(byte[] bases)
Creates a non-Ref allele.
|
static Allele |
Allele.create(byte[] bases,
boolean isRef)
Create a new Allele that includes bases and if tagged as the reference allele if isRef == true.
|
static Allele |
Allele.create(byte base,
boolean isRef) |
static Allele |
Allele.create(java.lang.String bases)
Creates a non-Ref allele.
|
static Allele |
Allele.create(java.lang.String bases,
boolean isRef) |
static Allele |
Allele.extend(Allele left,
byte[] right) |
Allele |
VariantContext.getAllele(byte[] allele) |
abstract Allele |
Genotype.getAllele(int i)
Get the ith allele in this genotype
|
Allele |
FastGenotype.getAllele(int i) |
Allele |
VariantContext.getAllele(java.lang.String allele) |
Allele |
VariantContext.getAltAlleleWithHighestAlleleCount() |
Allele |
VariantContext.getAlternateAllele(int i) |
static Allele |
Allele.getMatchingAllele(java.util.Collection<Allele> allAlleles,
byte[] alleleBases) |
Allele |
VariantContext.getReference() |
Modifier and Type | Method and Description |
---|---|
abstract java.util.List<Allele> |
Genotype.getAlleles() |
java.util.List<Allele> |
VariantContext.getAlleles()
Gets the alleles.
|
java.util.List<Allele> |
VariantContextBuilder.getAlleles() |
java.util.List<Allele> |
FastGenotype.getAlleles() |
java.util.List<Allele> |
VariantContext.getAlternateAlleles()
Gets the alternate alleles.
|
Modifier and Type | Method and Description |
---|---|
boolean |
Allele.basesMatch(Allele test) |
int |
Allele.compareTo(Allele other) |
int |
Genotype.countAllele(Allele allele)
Returns how many times allele appears in this genotype object?
|
static Allele |
Allele.create(Allele allele,
boolean ignoreRefState)
Creates a new allele based on the provided one.
|
boolean |
Allele.equals(Allele other,
boolean ignoreRefState)
Returns true if this and other are equal.
|
static Allele |
Allele.extend(Allele left,
byte[] right) |
void |
VariantContext.extraStrictValidation(Allele reportedReference,
Allele observedReference,
java.util.Set<java.lang.String> rsIDs)
Run all extra-strict validation tests on a Variant Context object
|
int |
VariantContext.getAlleleIndex(Allele allele)
Lookup the index of allele in this variant context
|
int |
VariantContext.getCalledChrCount(Allele a)
Returns the number of chromosomes carrying allele A in the genotypes
|
int |
VariantContext.getCalledChrCount(Allele a,
java.util.Set<java.lang.String> sampleIds)
Returns the number of chromosomes carrying allele A in the genotypes
|
int[] |
VariantContext.getGLIndecesOfAlternateAllele(Allele targetAllele) |
boolean |
VariantContext.hasAllele(Allele allele) |
boolean |
VariantContext.hasAllele(Allele allele,
boolean ignoreRefState) |
boolean |
VariantContext.hasAlternateAllele(Allele allele) |
boolean |
VariantContext.hasAlternateAllele(Allele allele,
boolean ignoreRefState) |
static boolean |
Allele.oneIsPrefixOfOther(Allele a1,
Allele a2) |
void |
VariantContext.validateReferenceBases(Allele reportedReference,
Allele observedReference) |
Modifier and Type | Method and Description |
---|---|
VariantContextBuilder |
VariantContextBuilder.alleles(java.util.Collection<Allele> alleles)
Tells this builder to use this collection of alleles for the resulting VariantContext
|
GenotypeBuilder |
GenotypeBuilder.alleles(java.util.List<Allele> alleles)
Set this genotype's alleles
|
VariantContextBuilder |
VariantContextBuilder.computeEndFromAlleles(java.util.List<Allele> alleles,
int start) |
static int |
VariantContextUtils.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
|
VariantContextBuilder |
VariantContextBuilder.computeEndFromAlleles(java.util.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.
|
static Genotype |
GenotypeBuilder.create(java.lang.String sampleName,
java.util.List<Allele> alleles) |
protected static Genotype |
GenotypeBuilder.create(java.lang.String sampleName,
java.util.List<Allele> alleles,
double[] gls) |
static Genotype |
GenotypeBuilder.create(java.lang.String sampleName,
java.util.List<Allele> alleles,
java.util.Map<java.lang.String,java.lang.Object> attributes) |
java.util.List<java.lang.Integer> |
VariantContext.getAlleleIndices(java.util.Collection<Allele> alleles)
Return the allele index #getAlleleIndex for each allele in alleles
|
double |
GenotypeLikelihoods.getLog10GQ(Genotype genotype,
java.util.List<Allele> vcAlleles) |
static Allele |
Allele.getMatchingAllele(java.util.Collection<Allele> allAlleles,
byte[] alleleBases) |
static boolean |
VariantContext.hasSymbolicAlleles(java.util.List<Allele> alleles) |
Constructor and Description |
---|
Allele(Allele allele,
boolean ignoreRefState)
Creates a new allele based on the provided one.
|
Constructor and Description |
---|
FastGenotype(java.lang.String sampleName,
java.util.List<Allele> alleles,
boolean isPhased,
int GQ,
int DP,
int[] AD,
int[] PL,
java.lang.String filters,
java.util.Map<java.lang.String,java.lang.Object> extendedAttributes)
The only way to make one of these, for use by GenotypeBuilder only
|
GenotypeBuilder(java.lang.String sampleName,
java.util.List<Allele> alleles)
Make a builder using sampleName and alleles for starting values
|
VariantContext(java.lang.String source,
java.lang.String ID,
java.lang.String contig,
long start,
long stop,
java.util.Collection<Allele> alleles,
GenotypesContext genotypes,
double log10PError,
java.util.Set<java.lang.String> filters,
java.util.Map<java.lang.String,java.lang.Object> attributes,
boolean fullyDecoded,
java.util.EnumSet<VariantContext.Validation> validationToPerform)
the actual constructor.
|
VariantContextBuilder(java.lang.String source,
java.lang.String contig,
long start,
long stop,
java.util.Collection<Allele> alleles)
Create an empty VariantContextBuilder where all values adopt their default values, but the bare min.
|
Modifier and Type | Field and Description |
---|---|
protected java.util.Map<java.lang.String,java.util.List<Allele>> |
AbstractVCFCodec.alleleMap |
Modifier and Type | Method and Description |
---|---|
protected static Allele |
AbstractVCFCodec.oneAllele(java.lang.String index,
java.util.List<Allele> alleles)
create a an allele from an index and an array of alleles
|
Modifier and Type | Method and Description |
---|---|
java.util.Map<Allele,java.lang.String> |
VCFEncoder.buildAlleleStrings(VariantContext vc) |
protected static java.util.List<Allele> |
AbstractVCFCodec.parseAlleles(java.lang.String ref,
java.lang.String alts,
int lineNo)
parse out the alleles
|
protected static java.util.List<Allele> |
AbstractVCFCodec.parseGenotypeAlleles(java.lang.String GT,
java.util.List<Allele> alleles,
java.util.Map<java.lang.String,java.util.List<Allele>> cache)
parse genotype alleles from the genotype string
|
Modifier and Type | Method and Description |
---|---|
void |
VCFEncoder.addGenotypeData(VariantContext vc,
java.util.Map<Allele,java.lang.String> alleleMap,
java.util.List<java.lang.String> genotypeFormatKeys,
java.lang.StringBuilder builder) |
LazyGenotypesContext.LazyData |
AbstractVCFCodec.createGenotypeMap(java.lang.String str,
java.util.List<Allele> alleles,
java.lang.String chr,
int pos)
create a genotype map
|
protected static Allele |
AbstractVCFCodec.oneAllele(java.lang.String index,
java.util.List<Allele> alleles)
create a an allele from an index and an array of alleles
|
protected static java.util.List<Allele> |
AbstractVCFCodec.parseGenotypeAlleles(java.lang.String GT,
java.util.List<Allele> alleles,
java.util.Map<java.lang.String,java.util.List<Allele>> cache)
parse genotype alleles from the genotype string
|
protected static java.util.List<Allele> |
AbstractVCFCodec.parseGenotypeAlleles(java.lang.String GT,
java.util.List<Allele> alleles,
java.util.Map<java.lang.String,java.util.List<Allele>> cache)
parse genotype alleles from the genotype string
|