Package | Description |
---|---|
htsjdk.variant.bcf2 | |
htsjdk.variant.variantcontext |
Modifier and Type | Method and Description |
---|---|
void |
BCF2GenotypeFieldDecoders.Decoder.decode(List<Allele> siteAlleles,
String field,
BCF2Decoder decoder,
byte typeDescriptor,
int numElements,
GenotypeBuilder[] gbs) |
Modifier and Type | Method and Description |
---|---|
GenotypeBuilder |
GenotypeBuilder.AD(int[] AD)
This genotype has this AD value
|
GenotypeBuilder |
GenotypeBuilder.alleles(List<Allele> alleles)
Set this genotype's alleles
|
GenotypeBuilder |
GenotypeBuilder.attribute(String key,
Object value)
This genotype has this attribute key / value pair.
|
GenotypeBuilder |
GenotypeBuilder.attributes(Map<String,Object> attributes)
This genotype has these attributes.
|
GenotypeBuilder |
GenotypeBuilder.copy(Genotype g)
Copy all of the values for this builder from Genotype g
|
GenotypeBuilder |
GenotypeBuilder.DP(int DP)
This genotype has this DP value
|
GenotypeBuilder |
GenotypeBuilder.filter(String filter)
Most efficient version of setting filters -- just set the filters string to filters
|
GenotypeBuilder |
GenotypeBuilder.filters(List<String> filters)
Tells this builder to make a Genotype object that has had filters applied,
which may be empty (passes) or have some value indicating the reasons
why it's been filtered.
|
GenotypeBuilder |
GenotypeBuilder.filters(String... filters)
varargs version of #filters
|
GenotypeBuilder |
GenotypeBuilder.GQ(int GQ) |
GenotypeBuilder |
GenotypeBuilder.log10PError(double pLog10Error)
Set the GQ with a log10PError value
|
GenotypeBuilder |
GenotypeBuilder.maxAttributes(int i)
Tell's this builder that we have at most these number of attributes
|
GenotypeBuilder |
GenotypeBuilder.name(String sampleName)
Set this genotype's name
|
GenotypeBuilder |
GenotypeBuilder.noAD()
This genotype has no AD value
|
GenotypeBuilder |
GenotypeBuilder.noAttributes()
Tells this builder to remove all extended attributes
|
GenotypeBuilder |
GenotypeBuilder.noDP()
This genotype has no DP value
|
GenotypeBuilder |
GenotypeBuilder.noGQ()
This genotype has no GQ value
|
GenotypeBuilder |
GenotypeBuilder.noPL()
This genotype has no PL value
|
GenotypeBuilder |
GenotypeBuilder.phased(boolean phased)
Is this genotype phased?
|
GenotypeBuilder |
GenotypeBuilder.PL(double[] GLs)
This genotype has this PL value, converted from double[].
|
GenotypeBuilder |
GenotypeBuilder.PL(int[] PL)
This genotype has this PL value, as int[].
|
GenotypeBuilder |
GenotypeBuilder.unfiltered()
This genotype is unfiltered
|