Package | Description |
---|---|
htsjdk.variant.bcf2 | |
htsjdk.variant.variantcontext | |
htsjdk.variant.variantcontext.filter | |
htsjdk.variant.variantcontext.writer | |
htsjdk.variant.vcf |
Modifier and Type | Method and Description |
---|---|
VariantContext |
BCF2Codec.decode(PositionalBufferedStream inputStream) |
Modifier and Type | Method and Description |
---|---|
java.lang.Class<VariantContext> |
BCF2Codec.getFeatureType() |
Modifier and Type | Method and Description |
---|---|
VariantContext |
VariantContext.fullyDecode(VCFHeader header,
boolean lenientDecoding)
Return a VC equivalent to this one but where all fields are fully decoded
See VariantContext document about fully decoded
|
VariantContext |
VariantContextBuilder.make()
Takes all of the builder data provided up to this point, and instantiates
a freshly allocated VariantContext with all of the builder data.
|
VariantContext |
VariantContextBuilder.make(boolean leaveModifyableAsIs) |
static VariantContext |
VariantContextUtils.sitesOnlyVariantContext(VariantContext vc)
Returns a newly allocated VC that is the same as VC, but without genotypes
|
VariantContext |
VariantContext.subContextFromSample(java.lang.String sampleName) |
VariantContext |
VariantContext.subContextFromSamples(java.util.Set<java.lang.String> sampleNames) |
VariantContext |
VariantContext.subContextFromSamples(java.util.Set<java.lang.String> sampleNames,
boolean rederiveAllelesFromGenotypes)
This method subsets down to a set of samples.
|
Modifier and Type | Method and Description |
---|---|
static java.util.Collection<VariantContext> |
VariantContextUtils.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
|
Modifier and Type | Method and Description |
---|---|
static double |
VariantContextUtils.calculateAltAlleleFrequency(VariantContext vc)
Computes the alternate allele frequency at the provided
VariantContext by dividing its "AN" by its "AC". |
static java.util.Map<java.lang.String,java.lang.Object> |
VariantContextUtils.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> |
VariantContextUtils.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
|
int |
VariantContextComparator.compare(VariantContext firstVariantContext,
VariantContext secondVariantContext) |
double |
GenotypeLikelihoods.getLog10GQ(Genotype genotype,
VariantContext context) |
static int |
VariantContextUtils.getSize(VariantContext vc) |
boolean |
VariantContext.hasSameAllelesAs(VariantContext other) |
boolean |
VariantContext.hasSameAlternateAllelesAs(VariantContext other) |
static java.util.Map<VariantContextUtils.JexlVCMatchExp,java.lang.Boolean> |
VariantContextUtils.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> |
VariantContextUtils.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 |
VariantContextUtils.match(VariantContext vc,
Genotype g,
VariantContextUtils.JexlVCMatchExp exp)
Returns true if exp match VC/g.
|
static boolean |
VariantContextUtils.match(VariantContext vc,
VariantContextUtils.JexlVCMatchExp exp)
Returns true if exp match VC.
|
static VariantContext |
VariantContextUtils.sitesOnlyVariantContext(VariantContext vc)
Returns a newly allocated VC that is the same as VC, but without genotypes
|
Modifier and Type | Method and Description |
---|---|
static java.util.Collection<VariantContext> |
VariantContextUtils.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
|
Constructor and Description |
---|
VariantContext(VariantContext other)
Copy constructor
|
VariantContextBuilder(VariantContext parent)
Returns a new builder based on parent -- the new VC will have all fields initialized
to their corresponding values in parent.
|
Modifier and Type | Method and Description |
---|---|
VariantContext |
FilteringIterator.next()
Returns the next element in the iteration.
|
Modifier and Type | Method and Description |
---|---|
java.util.Iterator<VariantContext> |
FilteringIterator.iterator()
function to satisfy the Iterable interface
|
Modifier and Type | Method and Description |
---|---|
boolean |
VariantContextFilter.test(VariantContext record)
Determines whether a VariantContext matches this filter
|
boolean |
CompoundFilter.test(VariantContext variantContext) |
boolean |
SnpFilter.test(VariantContext variantContext) |
boolean |
GenotypeQualityFilter.test(VariantContext variantContext) |
boolean |
PassingVariantFilter.test(VariantContext variantContext) |
boolean |
HeterozygosityFilter.test(VariantContext variantContext) |
Constructor and Description |
---|
FilteringIterator(java.util.Iterator<VariantContext> iterator,
VariantContextFilter filter)
Constructor of an iterator based on the provided iterator and predicate.
|
Modifier and Type | Method and Description |
---|---|
void |
VariantContextWriter.add(VariantContext vc) |
void |
AsyncVariantContextWriter.add(VariantContext vc) |
void |
BCF2FieldWriter.GenotypesWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.IGFGenotypesWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.FTGenotypesWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.GTWriter.addGenotype(BCF2Encoder encoder,
VariantContext vc,
Genotype g) |
void |
BCF2FieldWriter.done(BCF2Encoder encoder,
VariantContext vc) |
protected void |
SortingVariantContextWriter.noteCurrentRecord(VariantContext vc) |
int |
BCF2FieldEncoder.numElements(VariantContext vc) |
protected int |
BCF2FieldWriter.GenotypesWriter.numElements(VariantContext vc,
Genotype g) |
protected int |
BCF2FieldWriter.IGFGenotypesWriter.numElements(VariantContext vc,
Genotype g) |
protected int |
BCF2FieldWriter.FTGenotypesWriter.numElements(VariantContext vc,
Genotype g) |
int |
BCF2FieldEncoder.numElements(VariantContext vc,
java.lang.Object value)
A convenience access for the number of elements.
|
abstract void |
BCF2FieldWriter.SiteWriter.site(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.GenericSiteWriter.site(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.GenotypesWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.IntegerTypeGenotypesWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.IGFGenotypesWriter.start(BCF2Encoder encoder,
VariantContext vc) |
void |
BCF2FieldWriter.GTWriter.start(BCF2Encoder encoder,
VariantContext vc) |
protected void |
AsyncVariantContextWriter.synchronouslyWrite(VariantContext item) |
Modifier and Type | Method and Description |
---|---|
VariantContext |
VCFRecordCodec.decode() |
VariantContext |
AbstractVCFCodec.decode(java.lang.String line)
decode the line into a feature (VariantContext)
|
Modifier and Type | Method and Description |
---|---|
CloseableIterator<VariantContext> |
VCFFileReader.iterator()
Returns an iterator over all records in this VCF/BCF file.
|
CloseableIterator<VariantContext> |
VCFFileReader.query(java.lang.String chrom,
int start,
int end)
Queries for records within the region specified.
|
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) |
java.util.Map<Allele,java.lang.String> |
VCFEncoder.buildAlleleStrings(VariantContext vc) |
void |
VCFRecordCodec.encode(VariantContext context) |
java.lang.String |
VCFEncoder.encode(VariantContext context) |
int |
VCFCompoundHeaderLine.getCount(VariantContext vc)
Get the number of values expected for this header field, given the properties of VariantContext vc
If the count is a fixed count, return that.
|