java.lang.AutoCloseable
, java.io.Closeable
AllData
, TargetData
public interface Data
extends java.io.Closeable
Data
represents a sliding window of target VCF records
or a sliding window of reference and target VCF records.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() |
Returns
true if the sliding window of VCF records can advance
and returns false otherwise. |
void |
close() |
Releases any I/O resources controlled by this object.
|
GeneticMap |
genMap() |
Returns the genetic map.
|
boolean |
lastWindowOnChrom() |
Returns
true if the current window of VCF records is the last
window for the chromosome and returns false 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, or
null if there are no reference data |
java.util.List<HapPair> |
refHapPairs() |
Returns a list of the reference haplotype pairs for the current
window.
|
Samples |
refSamples() |
Returns the list of reference samples, or
null 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.
|
Pedigree ped()
GeneticMap genMap()
boolean lastWindowOnChrom()
true
if the current window of VCF records is the last
window for the chromosome and returns false
otherwise.true
if the current window of VCF records is the last
window for the chromosomeboolean canAdvanceWindow()
true
if the sliding window of VCF records can advance
and returns false
otherwise.true
if the sliding window of VCF records can advancevoid advanceWindowCm()
java.lang.IllegalArgumentException
- if a format error in the input data
is detectedjava.lang.IllegalStateException
- if
this.canAdvanceWindow() == false
int windowIndex()
int targetOverlap()
int overlap()
int nextOverlapStart()
this.nMarkers()
if the next marker window is from a
different chromosome.int nTargetMarkers()
int nTargetMarkersSoFar()
Markers targetMarkers()
int nMarkers()
int nMarkersSoFar()
Markers markers()
int targetMarkerIndex(int marker)
marker
- a marker indexjava.lang.IndexOutOfBoundsException
- if
marker < 0 || marker >= this.nMarkers()
int markerIndex(int targetMarker)
targetMarker
- a target data marker indexjava.lang.IndexOutOfBoundsException
- if
targetMarker < 0 || targetMarker >= this.nTargetMarkers()
int nTargetSamples()
Samples targetSamples()
int nRefSamples()
Samples refSamples()
null
if
there are no reference samples.null
if
there are no reference samplesint nAllSamples()
Samples allSamples()
this.targetSamples()
. Reference samples are listed last
in the same order as the list returned by this.refSamples()
.GT targGT()
GL
instance will contain no markers if
this.advanceWindow()
has not yet been invoked.java.util.List<HapPair> restrictedRefHapPairs()
this.advanceWindow()
has not yet been invoked.java.util.List<HapPair> refHapPairs()
this.advanceWindow()
has not yet been invoked.RefGT refGT()
null
if there are no reference datanull
if there are no reference dataRefGT restrictRefGT()
null
if there are no reference datanull
if there are no reference datavoid close()
close
in interface java.lang.AutoCloseable
close
in interface java.io.Closeable