Package beagleutil
Class PbwtUpdater
- java.lang.Object
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- beagleutil.PbwtUpdater
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public class PbwtUpdater extends java.lang.Object
Class
PbwtUpdater
updates prefix and divergence arrays using the positional Burrows-Wheeler transform (PBWT).Instances of
PbwtUpdater
are not thread-safe.Reference: Durbin, Richard (2014) Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT). Bioinformatics 30(9):166-1272. doi: 10.1093/bioinformatics/btu014
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Constructor Summary
Constructors Constructor Description PbwtUpdater(int nHaps)
Constructs a newPbwtUpdater
instance for the specified data.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
bwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix, int[] div)
Update the specified prefix and divergence arrays using the backward Positional Burrows-Wheeler Transform.void
fwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix, int[] div)
Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform.int
nHaps()
Returns the number of haplotypes.
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Method Detail
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nHaps
public int nHaps()
Returns the number of haplotypes.- Returns:
- the number of haplotypes
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fwdUpdate
public void fwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix, int[] div)
Update the specified prefix and divergence arrays using the forward Positional Burrows-Wheeler Transform. The contract for this method is undefined if the specifiedprefix
array is not a permutation of0, 1, 2, ..., (nHaps - 1)
, or if the elements of the specifieddiv
arrays are not all less than or equal to the specifiedmarker
.- Parameters:
rec
- the haplotype allelesnAlleles
- the number of allelesmarker
- the marker index for the specified haplotype allelesprefix
- the prefix arraydiv
- the divergence array- Throws:
java.lang.IllegalArgumentException
- ifnAlleles < 1
java.lang.IndexOutOfBoundsException
- if(rec.get[j] < 0 || rec.get(j) >= nAlleles)
for anyj
satisfying(0 <= j && j < this.nHaps())
java.lang.IndexOutOfBoundsException
- ifprefix.length >= this.nHaps()
java.lang.IndexOutOfBoundsException
- ifdiv.length >= this.nHaps()
java.lang.NullPointerException
- ifrec == null || prefix == null || div == null
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bwdUpdate
public void bwdUpdate(IntArray rec, int nAlleles, int marker, int[] prefix, int[] div)
Update the specified prefix and divergence arrays using the backward Positional Burrows-Wheeler Transform. The contract for this method is undefined if the specifiedprefix
array is not a permutation of0, 1, 2, ..., (nHaps - 1)
, or if the elements of the specifieddiv
arrays are not all greater than or equal to the specifiedmarker
.- Parameters:
rec
- the haplotype allelesnAlleles
- the number of allelesmarker
- the marker index for the specified haplotype allelesprefix
- the prefix arraydiv
- the divergence array- Throws:
java.lang.IllegalArgumentException
- ifnAlleles < 1
java.lang.IndexOutOfBoundsException
- if(rec.get[j] < 0 || rec.get(j) >= nAlleles)
for anyj
satisfying(0 <= j && j < this.nHaps())
java.lang.IndexOutOfBoundsException
- ifprefix.length >= this.nHaps()
java.lang.IndexOutOfBoundsException
- ifdiv.length >= this.nHaps()
java.lang.NullPointerException
- ifrec == null || prefix == null || div == null
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