Modifier and Type | Method and Description |
---|---|
void |
advanceWindow(int overlap,
int windowSize)
Advances the sliding window of VCF records, and returns the advanced
window.
|
static AllData |
allData(SampleFileIt<VcfEmission> refIt,
SampleFileIt<? extends VcfEmission> targetIt)
Constructs and returns a new
AllData instance from VCF records
returned by the specified SampleFileIt objects. |
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.
|
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 nonRefIndex)
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 |
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.
|
java.util.List<HapPair> |
refHapPairs()
Returns a list of the reference haplotype pairs for the current
window.
|
SampleHapPairs |
refSampleHapPairs()
Returns 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.
|
GL |
targetGL()
Returns the genotype likelihoods for the target samples
restricted to the target data markers in the current window.
|
int |
targetMarkerIndex(int refIndex)
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.
|
java.lang.String |
toString()
Returns a string representation of
this . |
int |
window()
Returns the current window index.
|
public static AllData allData(SampleFileIt<VcfEmission> refIt, SampleFileIt<? extends VcfEmission> targetIt)
AllData
instance from VCF records
returned by the specified SampleFileIt
objects.refIt
- an iterator that returns reference VCF recordstargetIt
- an iterator that returns target VCF recordsAllData
instance.java.lang.IllegalArgumentException
- if either the reference data or
target data contain no samplesjava.lang.IllegalArgumentException
- if a format error is detected
in a string VCF recordjava.lang.NullPointerException
- if refIt == null || targetIt == null
public boolean lastWindowOnChrom()
Data
true
if the current window of VCF records is the last
window for the chromosome and returns false
otherwise.lastWindowOnChrom
in interface Data
true
if the current window of VCF records is the last
window for the chromosomepublic boolean canAdvanceWindow()
Data
true
if the sliding window of VCF records can advance
and returns false
otherwise.canAdvanceWindow
in interface Data
true
if the sliding window of VCF records can advancepublic void advanceWindow(int overlap, int windowSize)
Data
advanceWindow
in interface Data
overlap
- the number of markers of overlapwindowSize
- the requested number of the markers in the window
immediately after the method returnspublic int window()
Data
advanceWindow()
method.public int targetOverlap()
Data
targetOverlap
in interface Data
public int overlap()
Data
public int nTargetMarkers()
Data
nTargetMarkers
in interface Data
public int nTargetMarkersSoFar()
Data
nTargetMarkersSoFar
in interface Data
public Markers targetMarkers()
Data
targetMarkers
in interface Data
public int nMarkers()
Data
public int nMarkersSoFar()
Data
nMarkersSoFar
in interface Data
public Markers markers()
Data
public int targetMarkerIndex(int refIndex)
Data
targetMarkerIndex
in interface Data
refIndex
- a marker indexpublic int markerIndex(int nonRefIndex)
Data
markerIndex
in interface Data
nonRefIndex
- a target data marker indexpublic int nTargetSamples()
Data
nTargetSamples
in interface Data
public Samples targetSamples()
Data
targetSamples
in interface Data
public int nRefSamples()
Data
nRefSamples
in interface Data
public Samples refSamples()
Data
null
if
there are no reference samples.refSamples
in interface Data
null
if
there are no reference samplespublic int nAllSamples()
Data
nAllSamples
in interface Data
public Samples allSamples()
Data
this.targetSamples()
. Reference samples are listed last
in the same order as the list returned by this.refSamples()
.allSamples
in interface Data
public GL targetGL()
Data
GL
instance will contain no markers if
this.advanceWindow()
has not yet been invoked.public java.util.List<HapPair> restrictedRefHapPairs()
Data
this.advanceWindow()
has not yet been invoked.restrictedRefHapPairs
in interface Data
public java.util.List<HapPair> refHapPairs()
Data
this.advanceWindow()
has not yet been invoked.refHapPairs
in interface Data
public SampleHapPairs refSampleHapPairs()
Data
null
if there are no reference samples or if
this.advanceWindow()
has not yet been invoked.refSampleHapPairs
in interface Data
null
if there
are no reference haplotype pairspublic void close()
Data
public java.lang.String toString()
this
. The exact
details of the representation are unspecified and subject to change.toString
in class java.lang.Object
this