Package vcf
Interface RefGTRec
- All Superinterfaces:
DuplicatesGTRec
,GTRec
,IntArray
,MarkerContainer
- All Known Implementing Classes:
LowMafRefDiallelicGTRec
,LowMafRefGTRec
,SeqCodedRefGTRec
Interface RefGTRec
represents represents phased genotype data
for one marker. For implementations of this interface, unless otherwise
specified in the implementation documentation, if the isAlleleCoded()
method returns false
, the majorAllele()
,
alleleCount()
, and hapIndex()
methods will be computationally
expensive with compute time proportional to the number of haplotypes.
Alternatively if the isAlleleCoded()
method returns
true
, the maps()
and map()
methods will be
computationally expensive with compute time proportional to the number
of haplotypes.
All instances of RefGTRec
are required to be immutable.
-
Method Summary
Modifier and TypeMethodDescriptionstatic RefGTRec
Returns an allele-codedRefGTRec
instance for the specified data.static RefGTRec
Constructs and returns a new allele-codedRefGTRec
instance from the specified data.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.static RefGTRec
hapCodedInstance
(Marker marker, Samples samples, int[][] hapIndices) Constructs and returns a new allele-codedRefGTRec
instance from the specified data.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.int
nMaps()
Returnsthis.maps().length
Methods inherited from interface vcf.MarkerContainer
marker
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Method Details
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alleleCodedInstance
Returns an allele-codedRefGTRec
instance for the specified data.- Parameters:
rec
- the phased, non-missing genotype data- Returns:
- an allele-coded
RefGTRec
instance for the specified data - Throws:
NullPointerException
- ifrec == null
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alleleCodedInstance
Constructs and returns a new allele-codedRefGTRec
instance from the specified data.- Parameters:
gtp
- a VCF record parser that extracts sample genotypes- Returns:
- an allele-coded
RefGTRec
instance - 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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hapCodedInstance
Constructs and returns a new allele-codedRefGTRec
instance from the specified data.- Parameters:
marker
- the markersamples
- the sampleshapIndices
- an array whosej
-th element isnull
ifj
is the major allele and otherwise is a list of haplotypes sorted in increasing order that carry thej
-th allele. If there is more than one allele with a maximal allele count, the major allele is the smallest allele with maximal allele count. If a haplotype is contained in a list for more than one non-major allele, the haplotype will be assumed to carry the smallest allele.- Returns:
- an allele-coded
RefGTRec
instance - Throws:
IllegalArgumentException
- if the(hapIndices[j] == null)
andj
is not the major allele or if(hapIndices[j] != null)
andj
is the major alleleIllegalArgumentException
- 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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hapIndices
int[][] hapIndices()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- 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
boolean isPhased(int sample) Returnstrue
.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Parameters:
sample
- the sample index- Returns:
true
- Throws:
IndexOutOfBoundsException
- ifsample < 0 || sample >= this.nSamples()
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isPhased
boolean isPhased()Returnstrue
.- Specified by:
isPhased
in interfaceDuplicatesGTRec
- Returns:
true
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isAlleleCoded
boolean isAlleleCoded()Returnstrue
if this instance stores the indices of haplotypes that carry non-major alleles, and returnsfalse
otherwise.- Returns:
true
if this instance stores the indices of haplotypes that carry non-major alleles
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majorAllele
int majorAllele()Returns the index of the major allele.- Returns:
- the index of the major allele
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alleleCounts
int[] alleleCounts()Returns an array of lengththis.nAlleles()
whosej
-th element is the allele count of thej
-th allele.- Returns:
- an array of allele counts
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alleleCount
int alleleCount(int allele) Returns the number of haplotypes that carry the specified non-major allele.- Parameters:
allele
- an allele index- Returns:
- the number of haplotypes that carry the specified non-major allele
- Throws:
IllegalArgumentException
- ifallele == this.majorAllele()
IndexOutOfBoundsException
- ifallele < 0 || allele >= this.nAlleles()
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hapIndex
int hapIndex(int allele, int copy) Returns index of the haplotype that carries the specified copy of the specified allele.- Parameters:
allele
- an allele indexcopy
- a copy index- Returns:
- index of the haplotype that carries the specified allele
- Throws:
IllegalArgumentException
- ifallele == this.majorAllele()
IndexOutOfBoundsException
- ifallele < 0 || allele >= this.nAlleles()
IndexOutOfBoundsException
- ifcopy < 0 || copy >= this.alleleCount(allele)
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isCarrier
boolean isCarrier(int allele, int hap) Returnstrue
if the specified haplotype carries the specified allele and returnfalse
otherwise.- Parameters:
allele
- an allele indexhap
- a haplotype index- Returns:
true
if the specified haplotype carries the specified allele- Throws:
IndexOutOfBoundsException
- ifhap < 0 || hap >= this.size()
IndexOutOfBoundsException
- ifallele < 0 || allele >= this.nAlleles()
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nMaps
int nMaps()Returnsthis.maps().length
- Returns:
- this.maps().length
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maps
IntArray[] maps()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
- Returns:
- an array of maps, which when composed map haplotype indices to alleles
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map
Returnsthis.maps()[index]
.- Parameters:
index
- the index inthis.maps()
- Returns:
this.maps()[index]
- Throws:
IndexOutOfBoundsException
- ifindex < 0 || index >= this.nMaps()
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