Package vcf
Class LowMafRefGTRec
java.lang.Object
vcf.LowMafRefGTRec
- All Implemented Interfaces:
IntArray
,DuplicatesGTRec
,GTRec
,MarkerContainer
,RefGTRec
Class LowMafRefGTRec
represent represents phased, non-missing
genotypes for a list of reference samples at a single marker.
Class LowMafRefGTRec
stores the haplotypes that carry each
non-major allele.
Instances of class LowMemRefGTRec
are immutable.
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Constructor Summary
ConstructorsConstructorDescriptionLowMafRefGTRec
(Marker marker, Samples samples, int[][] hapIndices) Constructs a newLowMafRefGTRec
instance from the specified data.LowMafRefGTRec
(RefGTRec rec) Constructs a newLowMafRefGTRec
instance from the specified data.Constructs a newLowMafRefGTRc
instance from the specified 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 haplotypes that carry the specified non-major allele.int[]
Returns an array of lengththis.nAlleles()
whosej
-th element is the allele count of thej
-th 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.int
hapIndex
(int allele, int copy) Returns index of the haplotype that carries the specified copy of the specified allele.int[][]
Returns an array whosej
-th element isnull
ifj
is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry thej
-th allele sorted in increasing orderboolean
Returnstrue
if this instance stores the indices of haplotypes that carry non-major alleles, and returnsfalse
otherwise.boolean
isCarrier
(int allele, int hap) Returnstrue
if the specified haplotype carries the specified allele and returnfalse
otherwise.boolean
isPhased()
Returnstrue
.boolean
isPhased
(int sample) Returnstrue
.int
Returns the index of the major allele.map
(int index) Returnsthis.maps()[index]
.IntArray[]
maps()
Returns an array of maps, which when composed map haplotype indices to alleles.marker()
Returns the marker.int
nMaps()
Returnsthis.maps().length
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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LowMafRefGTRec
Constructs a newLowMafRefGTRec
instance from the specified data.- Parameters:
rec
- the phased, non-missing genotype data- Throws:
NullPointerException
- ifrec == null
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LowMafRefGTRec
Constructs a newLowMafRefGTRc
instance from the specified data.- Parameters:
gtp
- a VCF record parser that extracts sample genotypes- Throws:
IllegalArgumentException
- if the VCF record contains an unphased genotype or missing alleleIllegalArgumentException
- if a format error is detected in the VCF recordNullPointerException
- ifgtp == null
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LowMafRefGTRec
Constructs a newLowMafRefGTRec
instance from the specified data. The specifiedhapIndices
array is required to contain exactly onenull
element. Thenull
element should be the major allele because this is most memory-efficient, but this requirement is not enforced. A haplotype index should be an element of only one array inhapIndices
. If a haplotype index is an element of more than one array inhapIndices
, it is assigned to the array with smallest index.- Parameters:
marker
- the markersamples
- the sampleshapIndices
- whosej
-th element is a list of haplotypes sorted in increasing order that carry thej
-th allele, or isnull
- Throws:
IllegalArgumentException
- if the(hapIndices
does not contain exactly onenull
elementIllegalArgumentException
- if any non-null element ofhapIndices
is not a sorted list of distinct haplotype indices between 0 (inclusive) and2*samples.size()
(exclusive)IllegalArgumentException
- ifmarker.nAlleles() != hapIndices.length
NullPointerException
- ifmarker == null || samples == null || hapIndices == null
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Method Details
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hapIndices
public int[][] hapIndices()Description copied from interface:RefGTRec
Returns an array whosej
-th element isnull
ifj
is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry thej
-th allele sorted in increasing order- Specified by:
hapIndices
in interfaceRefGTRec
- Returns:
- an array whose
j
-th element isnull
ifj
is the major allele with lowest index, and otherwise is an array of indices of haplotypes that carry thej
-th allele sorted in increasing order
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isPhased
public boolean isPhased(int sample) Description copied from interface:RefGTRec
Returnstrue
.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Specified by:
isPhased
in interfaceRefGTRec
- Parameters:
sample
- the sample index- Returns:
true
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isPhased
public boolean isPhased()Returnstrue
.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Specified by:
isPhased
in interfaceRefGTRec
- Returns:
true
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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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isAlleleCoded
public boolean isAlleleCoded()Description copied from interface:RefGTRec
Returnstrue
if this instance stores the indices of haplotypes that carry non-major alleles, and returnsfalse
otherwise.- Specified by:
isAlleleCoded
in interfaceRefGTRec
- Returns:
true
if this instance stores the indices of haplotypes that carry non-major alleles
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majorAllele
public int majorAllele()Description copied from interface:RefGTRec
Returns the index of the major allele.- Specified by:
majorAllele
in interfaceRefGTRec
- Returns:
- the index of the major allele
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alleleCounts
public int[] alleleCounts()Description copied from interface:RefGTRec
Returns an array of lengththis.nAlleles()
whosej
-th element is the allele count of thej
-th allele.- Specified by:
alleleCounts
in interfaceRefGTRec
- Returns:
- an array of allele counts
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alleleCount
public int alleleCount(int allele) Description copied from interface:RefGTRec
Returns the number of haplotypes that carry the specified non-major allele.- Specified by:
alleleCount
in interfaceRefGTRec
- Parameters:
allele
- an allele index- Returns:
- the number of haplotypes that carry the specified non-major allele
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hapIndex
public int hapIndex(int allele, int copy) Description copied from interface:RefGTRec
Returns index of the haplotype that carries the specified copy of the specified allele. -
isCarrier
public boolean isCarrier(int allele, int hap) Description copied from interface:RefGTRec
Returnstrue
if the specified haplotype carries the specified allele and returnfalse
otherwise. -
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. -
nMaps
public int nMaps()Description copied from interface:RefGTRec
Returnsthis.maps().length
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maps
Description copied from interface:RefGTRec
Returns an array of maps, which when composed map haplotype indices to alleles. The allele on haplotypeh
is determined by the following calculation:IntArray[] maps = this.maps(); int value = maps[0].get(h); for (int j=1; j<maps.length; ++j) { value = indexArrays[j].get(value); } int allele = value
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map
Description copied from interface:RefGTRec
Returnsthis.maps()[index]
.
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