Package vcf
Class BitArrayGTRec
- java.lang.Object
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- vcf.BitArrayGTRec
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- All Implemented Interfaces:
IntArray
,DuplicatesGTRec
,GTRec
,MarkerContainer
public final class BitArrayGTRec extends java.lang.Object implements GTRec
Class
BitArrayGT
represents genotypes for a list of samples at a single marker. Instances of classBitArrayGTRec
store haplotype alleles and flags to indicate missing genotypes in bit sets. All genotypes are considered to be unphased if any sample has an unphased or missing genotype.tInstances of class
BitArrayGTRec
are immutable.
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Constructor Summary
Constructors Constructor Description BitArrayGTRec(VcfRecGTParser recParser)
Constructs a newBitArrayGT
instance representing the specified VCF record's GT format field data.BitArrayGTRec(VcfRecGTParser.HapListRep hlr)
Constructs a newBitArrayGT
instance representing the specified VCF record's GT format field data.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
allele1(int sample)
Returns the first allele for the specified sample or -1 if the allele is missing.int
allele2(int sample)
Returns the second allele for the specified sample or -1 if the allele is missing.int[]
alleles()
Returns an array of lengththis.size()
whosej
-th element is equal tothis.allele(j
}int
get(int hap)
Returns the specified allele for the specified haplotype or -1 if the allele is missing.boolean
isPhased()
Returnstrue
if every genotype for each sample is a phased, non-missing genotype, and returnsfalse
otherwise.boolean
isPhased(int sample)
Returnstrue
if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.Marker
marker()
Returns the marker.Samples
samples()
Returns the list of samples.int
size()
Returns the number of haplotypes.java.lang.String
toString()
Returns the data represented bythis
as a VCF record with a GT format field.
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Constructor Detail
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BitArrayGTRec
public BitArrayGTRec(VcfRecGTParser recParser)
Constructs a newBitArrayGT
instance representing the specified VCF record's GT format field data.- Parameters:
recParser
- the VCF record genotype data- Throws:
java.lang.IllegalArgumentException
- if a format error is detected in the VCF recordjava.lang.NullPointerException
- ifrecParser == null
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BitArrayGTRec
public BitArrayGTRec(VcfRecGTParser.HapListRep hlr)
Constructs a newBitArrayGT
instance representing the specified VCF record's GT format field data.- Parameters:
hlr
- the VCF record genotype data- Throws:
java.lang.IllegalArgumentException
- if a format error is detected in the VCF recordjava.lang.NullPointerException
- ifhlr == null
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Method Detail
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samples
public Samples samples()
Description copied from interface:GTRec
Returns the list of samples.
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size
public int size()
Description copied from interface:DuplicatesGTRec
Returns the number of haplotypes.- Specified by:
size
in interfaceDuplicatesGTRec
- Specified by:
size
in interfaceIntArray
- Returns:
- the number of haplotypes
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marker
public Marker marker()
Description copied from interface:MarkerContainer
Returns the marker.- Specified by:
marker
in interfaceMarkerContainer
- Returns:
- the marker
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isPhased
public boolean isPhased()
Description copied from interface:DuplicatesGTRec
Returnstrue
if every genotype for each sample is a phased, non-missing genotype, and returnsfalse
otherwise.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Returns:
true
if the genotype for each sample is a phased, non-missing genotype
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isPhased
public boolean isPhased(int sample)
Description copied from interface:DuplicatesGTRec
Returnstrue
if the genotype for the specified sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Parameters:
sample
- a sample index- Returns:
true
if the genotype for the specified sample is a phased, nonmissing genotype
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allele1
public int allele1(int sample)
Description copied from interface:DuplicatesGTRec
Returns the first allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.- Specified by:
allele1
in interfaceDuplicatesGTRec
- Parameters:
sample
- a sample index- Returns:
- the first allele for the specified sample
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allele2
public int allele2(int sample)
Description copied from interface:DuplicatesGTRec
Returns the second allele for the specified sample or -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered ifthis.unphased(marker, sample) == false
.- Specified by:
allele2
in interfaceDuplicatesGTRec
- Parameters:
sample
- a sample index- Returns:
- the second allele for the specified sample
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get
public int get(int hap)
Description copied from interface:DuplicatesGTRec
Returns the specified allele for the specified haplotype or -1 if the allele is missing. The two alleles for a sample at a marker are arbitrarily ordered ifthis.unphased(marker, hap/2) == false
.- Specified by:
get
in interfaceDuplicatesGTRec
- Specified by:
get
in interfaceIntArray
- Parameters:
hap
- a haplotype index- Returns:
- the specified allele for the specified sample
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alleles
public int[] alleles()
Description copied from interface:DuplicatesGTRec
Returns an array of lengththis.size()
whosej
-th element is equal tothis.allele(j
}- Specified by:
alleles
in interfaceDuplicatesGTRec
- Returns:
- an array of length
this.size()
whosej
-th element is equal tothis.allele(j
}
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toString
public java.lang.String toString()
Returns the data represented bythis
as a VCF record with a GT format field. The returned VCF record will have missing QUAL and INFO fields, will have "PASS" in the filter field, and will have a GT format field.- Overrides:
toString
in classjava.lang.Object
- Returns:
- the data represented by
this
as a VCF record with a GT format field
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