Package haplotype
Class WrappedHapPair
- java.lang.Object
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- haplotype.WrappedHapPair
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Constructor Summary
Constructors Constructor Description WrappedHapPair(GT phasedGT, int hapPair)
Creates aWrappedHapPair
instance representing the specified haplotype pair.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
allele1(int marker)
Returns the first allele for the specified marker.int
allele2(int marker)
Returns the second allele for the specified marker.int
idIndex()
Returns the sample identifier index.Marker
marker(int marker)
Returns the specified marker.Markers
markers()
Returns the markers.int
nMarkers()
Returns the number of markers.
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Constructor Detail
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WrappedHapPair
public WrappedHapPair(GT phasedGT, int hapPair)
Creates aWrappedHapPair
instance representing the specified haplotype pair.- Parameters:
phasedGT
- theRefGTWindow
object that will be "wrapped" bythis
hapPair
- a haplotype pair index- Throws:
java.lang.IllegalArgumentException
- ifphasedGT.isPhased() == false
java.lang.IllegalArgumentException
- ifhapPair < 0 || hapPair >= sampleHapPairs.nHapPairs()
java.lang.NullPointerException
- ifsampleHapPairs == null
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Method Detail
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allele1
public int allele1(int marker)
Description copied from interface:HapPair
Returns the first allele for the specified marker.
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allele2
public int allele2(int marker)
Description copied from interface:HapPair
Returns the second allele for the specified marker.
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marker
public Marker marker(int marker)
Description copied from interface:HapPair
Returns the specified marker.
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nMarkers
public int nMarkers()
Description copied from interface:HapPair
Returns the number of markers.
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