Package vcf
Class LowMafGTRec
java.lang.Object
vcf.LowMafGTRec
- All Implemented Interfaces:
IntArray
,DuplicatesGTRec
,GTRec
,MarkerContainer
Class LowMafGTRc
stores genotypes for a list of samples
at a marker. Instances of class LowMafGTRec
store lists of
haplotypes carrying each non-major or missing allele. All genotypes are
considered to be unphased if any sample has an unphased or missing
genotype.
Instances of class LowMafGTRec
are immutable.
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Constructor Summary
ConstructorsConstructorDescriptionLowMafGTRec
(VcfRecGTParser.HapListRep listRep) Constructs a newLowMafGTRec
representing the specified VCF record's GT format field data. -
Method Summary
Modifier and TypeMethodDescriptionint
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
alleleCount
(int allele) Returns the number of copies of the specified allele.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.int
Returns the major allele.marker()
Returns the marker.samples()
Returns the list of samples.int
size()
Returns the number of haplotypes.toString()
Returns the data represented bythis
as a VCF record with a GT format field.
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Constructor Details
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LowMafGTRec
Constructs a newLowMafGTRec
representing the specified VCF record's GT format field data.- Parameters:
listRep
- the VCF record genotype data- Throws:
NullPointerException
- iflistRep == null
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Method Details
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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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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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samples
Description copied from interface:GTRec
Returns the list of samples. -
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
Description copied from interface:MarkerContainer
Returns the marker.- Specified by:
marker
in interfaceMarkerContainer
- Returns:
- the marker
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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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majorAllele
public int majorAllele()Returns the major allele. If there are two major alleles with the same allele count, the smaller allele is returned.- Returns:
- the major allele
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alleleCount
public int alleleCount(int allele) Returns the number of copies of the specified allele.- Parameters:
allele
- an allele- Returns:
- the number of copies of the specified allele
- Throws:
IndexOutOfBoundsException
- ifallele < 0 || allele >= this.marker().nAlleles()
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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.
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