Package vcf
Interface Data
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- All Superinterfaces:
java.lang.AutoCloseable
,java.io.Closeable
- All Known Implementing Classes:
AllData
,TargetData
public interface Data extends java.io.Closeable
InterfaceData
represents a sliding window of target VCF records or a sliding window of reference and target VCF records.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
advanceWindowCm()
Advances the sliding window of VCF records.Samples
allSamples()
Returns a list of all target and reference samples.boolean
canAdvanceWindow()
Returnstrue
if the sliding window of VCF records can advance and returnsfalse
otherwise.void
close()
Releases any I/O resources controlled by this object.GeneticMap
genMap()
Returns the genetic map.boolean
lastWindowOnChrom()
Returnstrue
if the current window of VCF records is the last window for the chromosome and returnsfalse
otherwise.int
markerIndex(int targetMarker)
Returns the marker index corresponding to the specified target data marker.Markers
markers()
Returns the list of markers in the current window.int
nAllSamples()
Returns the total number of reference and target samples.int
nextOverlapStart()
Returns the first marker index in the overlap between this marker window and the next marker window.int
nMarkers()
Returns the number of markers in the current window.int
nMarkersSoFar()
Returns the number of markers in the union of the current window and all previous windows.int
nRefSamples()
Returns the number of reference samples.int
nTargetMarkers()
Returns the number of target data markers in the current window.int
nTargetMarkersSoFar()
Returns the number of target VCF records in the union of the current window and all previous windows.int
nTargetSamples()
Returns the number of target samples.int
overlap()
Returns the number of VCF records in the overlap between the current window and the previous window.Pedigree
ped()
Returns the pedigree.RefGT
refGT()
Returns the phased, nonmissing reference genotype data for the current window, ornull
if there are no reference datajava.util.List<HapPair>
refHapPairs()
Returns a list of the reference haplotype pairs for the current window.Samples
refSamples()
Returns the list of reference samples, ornull
if there are no reference samples.java.util.List<HapPair>
restrictedRefHapPairs()
Returns a list of reference haplotype pairs that are restricted to the target data markers in the current window.RefGT
restrictRefGT()
Returns the phased, nonmissing reference genotype data for the target data markers in the current window.int
targetMarkerIndex(int marker)
Returns the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists.Markers
targetMarkers()
Returns the list of target data markers in the current window.int
targetOverlap()
Returns the number of target data markers in the overlap between the current marker window and the previous marker window.Samples
targetSamples()
Returns the list of target samples.GT
targGT()
Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window.int
windowIndex()
Returns the current window index.
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Method Detail
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ped
Pedigree ped()
Returns the pedigree.- Returns:
- the pedigree
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genMap
GeneticMap genMap()
Returns the genetic map.- Returns:
- the genetic map
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lastWindowOnChrom
boolean lastWindowOnChrom()
Returnstrue
if the current window of VCF records is the last window for the chromosome and returnsfalse
otherwise.- Returns:
true
if the current window of VCF records is the last window for the chromosome
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canAdvanceWindow
boolean canAdvanceWindow()
Returnstrue
if the sliding window of VCF records can advance and returnsfalse
otherwise.- Returns:
true
if the sliding window of VCF records can advance
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advanceWindowCm
void advanceWindowCm()
Advances the sliding window of VCF records.- Throws:
java.lang.IllegalArgumentException
- if a format error in the input data is detectedjava.lang.IllegalStateException
- ifthis.canAdvanceWindow() == false
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windowIndex
int windowIndex()
Returns the current window index. The first window has index 1.- Returns:
- the current window index
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targetOverlap
int targetOverlap()
Returns the number of target data markers in the overlap between the current marker window and the previous marker window. Returns 0 if the current marker window is the first marker window.- Returns:
- the number of target data markers in the overlap between the current marker window and the previous marker window
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overlap
int overlap()
Returns the number of VCF records in the overlap between the current window and the previous window. Returns 0 if the current window is the first window.- Returns:
- the number of VCF records in the overlap between the current window and the previous window
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nextOverlapStart
int nextOverlapStart()
Returns the first marker index in the overlap between this marker window and the next marker window. Returnsthis.nMarkers()
if the next marker window is from a different chromosome.- Returns:
- the first marker index in the overlap between this marker window and the next marker window
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nTargetMarkers
int nTargetMarkers()
Returns the number of target data markers in the current window.- Returns:
- the number of target data markers in the current window
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nTargetMarkersSoFar
int nTargetMarkersSoFar()
Returns the number of target VCF records in the union of the current window and all previous windows.- Returns:
- the number of target VCF records in the union of the current window and all previous windows
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targetMarkers
Markers targetMarkers()
Returns the list of target data markers in the current window.- Returns:
- the list of target data markers in the current window
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nMarkers
int nMarkers()
Returns the number of markers in the current window.- Returns:
- the number of markers in the current window
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nMarkersSoFar
int nMarkersSoFar()
Returns the number of markers in the union of the current window and all previous windows.- Returns:
- the number of markers in the union of the current window and all previous windows
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markers
Markers markers()
Returns the list of markers in the current window.- Returns:
- the list of markers in the current window
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targetMarkerIndex
int targetMarkerIndex(int marker)
Returns the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists. Indices are with respect to the current window.- Parameters:
marker
- a marker index- Returns:
- the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists
- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
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markerIndex
int markerIndex(int targetMarker)
Returns the marker index corresponding to the specified target data marker. Indices are with respect to the current window.- Parameters:
targetMarker
- a target data marker index- Returns:
- the marker index corresponding to the specified target data marker
- Throws:
java.lang.IndexOutOfBoundsException
- iftargetMarker < 0 || targetMarker >= this.nTargetMarkers()
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nTargetSamples
int nTargetSamples()
Returns the number of target samples.- Returns:
- the number of target samples
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targetSamples
Samples targetSamples()
Returns the list of target samples.- Returns:
- the list of target samples
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nRefSamples
int nRefSamples()
Returns the number of reference samples.- Returns:
- the number of reference samples
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refSamples
Samples refSamples()
Returns the list of reference samples, ornull
if there are no reference samples.- Returns:
- the list of reference samples, or
null
if there are no reference samples
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nAllSamples
int nAllSamples()
Returns the total number of reference and target samples.- Returns:
- the total number of reference and target samples
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allSamples
Samples allSamples()
Returns a list of all target and reference samples. Target samples are listed first in the same order as the list returned bythis.targetSamples()
. Reference samples are listed last in the same order as the list returned bythis.refSamples()
.- Returns:
- a list of all target and reference samples
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targGT
GT targGT()
Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window. The returnedGL
instance will contain no markers ifthis.advanceWindow()
has not yet been invoked.- Returns:
- the genotype likelihoods for the target samples restricted to the target data markers in the current window
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restrictedRefHapPairs
java.util.List<HapPair> restrictedRefHapPairs()
Returns a list of reference haplotype pairs that are restricted to the target data markers in the current window. The returned list will be empty if there are no reference samples or ifthis.advanceWindow()
has not yet been invoked.- Returns:
- a list of reference haplotype pairs that are restricted to the target data markers
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refHapPairs
java.util.List<HapPair> refHapPairs()
Returns a list of the reference haplotype pairs for the current window. The returned list will be empty if there are no reference samples or ifthis.advanceWindow()
has not yet been invoked.- Returns:
- a list of the reference haplotype pairs
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refGT
RefGT refGT()
Returns the phased, nonmissing reference genotype data for the current window, ornull
if there are no reference data- Returns:
- the reference genotype data for the current window or
null
if there are no reference data
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restrictRefGT
RefGT restrictRefGT()
Returns the phased, nonmissing reference genotype data for the target data markers in the current window. Returnsnull
if there are no reference data- Returns:
- the reference genotype data for the target data markers
in the current window or
null
if there are no reference data
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close
void close()
Releases any I/O resources controlled by this object.- Specified by:
close
in interfacejava.lang.AutoCloseable
- Specified by:
close
in interfacejava.io.Closeable
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