public final class GenotypeBuilder extends Object
Constructor | Description |
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GenotypeBuilder() |
Create a empty builder.
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GenotypeBuilder(Genotype g) |
Create a new builder starting with the values in Genotype g
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GenotypeBuilder(String sampleName) |
Create a builder using sampleName.
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GenotypeBuilder(String sampleName,
List<Allele> alleles) |
Make a builder using sampleName and alleles for starting values
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Modifier and Type | Method | Description |
---|---|---|
GenotypeBuilder |
AD(int[] AD) |
This genotype has this AD value
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GenotypeBuilder |
alleles(List<Allele> alleles) |
Set this genotype's alleles
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GenotypeBuilder |
attribute(String key,
Object value) |
This genotype has this attribute key / value pair.
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GenotypeBuilder |
attributes(Map<String,Object> attributes) |
This genotype has these attributes.
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GenotypeBuilder |
copy(Genotype g) |
Copy all of the values for this builder from Genotype g
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static Genotype |
create(String sampleName,
List<Allele> alleles) |
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protected static Genotype |
create(String sampleName,
List<Allele> alleles,
double[] gls) |
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static Genotype |
create(String sampleName,
List<Allele> alleles,
Map<String,Object> attributes) |
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static Genotype |
createMissing(String sampleName,
int ploidy) |
Create a new Genotype object for a sample that's missing from the VC (i.e., in
the output header).
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GenotypeBuilder |
DP(int DP) |
This genotype has this DP value
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GenotypeBuilder |
filter(String filter) |
Most efficient version of setting filters -- just set the filters string to filters
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GenotypeBuilder |
filters(String... filters) |
varargs version of #filters
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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.
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GenotypeBuilder |
GQ(int GQ) |
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GenotypeBuilder |
log10PError(double pLog10Error) |
Set the GQ with a log10PError value
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Genotype |
make() |
Create a new Genotype object using the values set in this builder.
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Genotype |
makeWithShallowCopy() |
Create a new Genotype object using the values set in this builder, and perform a
shallow copy of reference types to allow safer re-use of this builder
After creation the values in this builder can be modified and more Genotypes
created.
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GenotypeBuilder |
maxAttributes(int i) |
Tell's this builder that we have at most these number of attributes
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GenotypeBuilder |
name(String sampleName) |
Set this genotype's name
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GenotypeBuilder |
noAD() |
This genotype has no AD value
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GenotypeBuilder |
noAttributes() |
Tells this builder to remove all extended attributes
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GenotypeBuilder |
noDP() |
This genotype has no DP value
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GenotypeBuilder |
noGQ() |
This genotype has no GQ value
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GenotypeBuilder |
noPL() |
This genotype has no PL value
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GenotypeBuilder |
phased(boolean phased) |
Is this genotype phased?
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GenotypeBuilder |
PL(double[] GLs) |
This genotype has this PL value, converted from double[].
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GenotypeBuilder |
PL(int[] PL) |
This genotype has this PL value, as int[].
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void |
reset(boolean keepSampleName) |
Reset all of the builder attributes to their defaults.
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GenotypeBuilder |
unfiltered() |
This genotype is unfiltered
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public GenotypeBuilder()
public GenotypeBuilder(String sampleName)
sampleName
- public GenotypeBuilder(String sampleName, List<Allele> alleles)
sampleName
- alleles
- public GenotypeBuilder(Genotype g)
g
- public static Genotype create(String sampleName, List<Allele> alleles, Map<String,Object> attributes)
public static Genotype createMissing(String sampleName, int ploidy)
sampleName
- the name of this samplepublic GenotypeBuilder copy(Genotype g)
g
- public final void reset(boolean keepSampleName)
public Genotype make()
makeWithShallowCopy()
to safely re-use the same builder object
multiple times.public Genotype makeWithShallowCopy()
public GenotypeBuilder name(String sampleName)
sampleName
- public GenotypeBuilder alleles(List<Allele> alleles)
alleles
- public GenotypeBuilder phased(boolean phased)
phased
- public GenotypeBuilder GQ(int GQ)
public GenotypeBuilder log10PError(double pLog10Error)
pLog10Error
- public GenotypeBuilder noGQ()
public GenotypeBuilder noAD()
public GenotypeBuilder noDP()
public GenotypeBuilder noPL()
public GenotypeBuilder DP(int DP)
public GenotypeBuilder AD(int[] AD)
public GenotypeBuilder PL(int[] PL)
public GenotypeBuilder PL(double[] GLs)
public GenotypeBuilder attributes(Map<String,Object> attributes)
public GenotypeBuilder noAttributes()
public GenotypeBuilder attribute(String key, Object value)
public GenotypeBuilder filters(List<String> filters)
filters
- non-null list of filters. empty list => PASSpublic GenotypeBuilder filters(String... filters)
filters
- public GenotypeBuilder filter(String filter)
filter
- if filters == null or filters.equals("PASS") => genotype is PASSpublic GenotypeBuilder unfiltered()
public GenotypeBuilder maxAttributes(int i)