Package vcf

Class AllData

java.lang.Object

vcf.AllData

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, Data

public class AllData
extends java.lang.Object
implements Data

Class AllData represents a sliding window of reference and target VCF recList.

Instances of class AllData are not thread-safe.

Method Summary

Modifier and Type	Method	Description
void	advanceWindowCm()	Advances the sliding window of VCF records.
static AllData	allData(java.util.function.Supplier<SampleFileIt<RefGTRec>> supplier, SampleFileIt<GTRec> targIt, Par par)	Constructs and returns a new AllData instance from VCF recList 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.
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 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	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 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.
GT	targGT()	Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window.
java.lang.String	toString()	Returns a string representation of this.
int	windowIndex()	Returns the current window index.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

allData

public static AllData allData(java.util.function.Supplier<SampleFileIt<RefGTRec>> supplier,
                              SampleFileIt<GTRec> targIt,
                              Par par)

Constructs and returns a new AllData instance from VCF recList returned by the specified SampleFileIt objects.

Parameters:

supplier - an object to supply the reference file iterator

targIt - an iterator that returns target VCF recList

par - the command line parameters

Returns:

a new AllData instance

Throws:

java.lang.IllegalArgumentException - if either the reference data or target data contain no samples

java.lang.IllegalArgumentException - if a format error is detected in a string VCF record

java.lang.IllegalArgumentException - if overlap < 0 || Float.isFinite(overlap) == false

java.lang.IllegalArgumentException - if window <= overlap || Float.isFinite(window) == false

java.lang.NullPointerException - if refIt == null || targetIt == null || genMap == null

ped

public Pedigree ped()

Description copied from interface: Data

Returns the pedigree.

Specified by:

ped in interface Data

Returns:

the pedigree

genMap

public GeneticMap genMap()

Description copied from interface: Data

Returns the genetic map.

Specified by:

genMap in interface Data

Returns:

the genetic map

lastWindowOnChrom

public boolean lastWindowOnChrom()

Description copied from interface: Data

Returns true if the current window of VCF records is the last window for the chromosome and returns false otherwise.

Specified by:

lastWindowOnChrom in interface Data

Returns:

true if the current window of VCF records is the last window for the chromosome

canAdvanceWindow

public boolean canAdvanceWindow()

Description copied from interface: Data

Returns true if the sliding window of VCF records can advance and returns false otherwise.

Specified by:

canAdvanceWindow in interface Data

Returns:

true if the sliding window of VCF records can advance

advanceWindowCm

public void advanceWindowCm()

Description copied from interface: Data

Advances the sliding window of VCF records.

Specified by:

advanceWindowCm in interface Data

windowIndex

public int windowIndex()

Description copied from interface: Data

Returns the current window index. The first window has index 1.

Specified by:

windowIndex in interface Data

Returns:

the current window index

targetOverlap

public int targetOverlap()

Description copied from interface: Data

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.

Specified by:

targetOverlap in interface Data

Returns:

the number of target data markers in the overlap between the current marker window and the previous marker window

overlap

public int overlap()

Description copied from interface: Data

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.

Specified by:

overlap in interface Data

Returns:

the number of VCF records in the overlap between the current window and the previous window

nextOverlapStart

public int nextOverlapStart()

Description copied from interface: Data

Returns the first marker index in the overlap between this marker window and the next marker window. Returns this.nMarkers() if the next marker window is from a different chromosome.

Specified by:

nextOverlapStart in interface Data

Returns:

the first marker index in the overlap between this marker window and the next marker window

nTargetMarkers

public int nTargetMarkers()

Description copied from interface: Data

Returns the number of target data markers in the current window.

Specified by:

nTargetMarkers in interface Data

Returns:

the number of target data markers in the current window

nTargetMarkersSoFar

public int nTargetMarkersSoFar()

Description copied from interface: Data

Returns the number of target VCF records in the union of the current window and all previous windows.

Specified by:

nTargetMarkersSoFar in interface Data

Returns:

the number of target VCF records in the union of the current window and all previous windows

targetMarkers

public Markers targetMarkers()

Description copied from interface: Data

Returns the list of target data markers in the current window.

Specified by:

targetMarkers in interface Data

Returns:

the list of target data markers in the current window

nMarkers

public int nMarkers()

Description copied from interface: Data

Returns the number of markers in the current window.

Specified by:

nMarkers in interface Data

Returns:

the number of markers in the current window

nMarkersSoFar

public int nMarkersSoFar()

Description copied from interface: Data

Returns the number of markers in the union of the current window and all previous windows.

Specified by:

nMarkersSoFar in interface Data

Returns:

the number of markers in the union of the current window and all previous windows

markers

public Markers markers()

Description copied from interface: Data

Returns the list of markers in the current window.

Specified by:

markers in interface Data

Returns:

the list of markers in the current window

targetMarkerIndex

public int targetMarkerIndex(int refIndex)

Description copied from interface: Data

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.

Specified by:

targetMarkerIndex in interface Data

Parameters:

refIndex - a marker index

Returns:

the target data marker index corresponding to the specified marker, or returns -1 if no corresponding target data marker exists

markerIndex

public int markerIndex(int nonRefIndex)

Description copied from interface: Data

Returns the marker index corresponding to the specified target data marker. Indices are with respect to the current window.

Specified by:

markerIndex in interface Data

Parameters:

nonRefIndex - a target data marker index

Returns:

the marker index corresponding to the specified target data marker

nTargetSamples

public int nTargetSamples()

Description copied from interface: Data

Returns the number of target samples.

Specified by:

nTargetSamples in interface Data

Returns:

the number of target samples

targetSamples

public Samples targetSamples()

Description copied from interface: Data

Returns the list of target samples.

Specified by:

targetSamples in interface Data

Returns:

the list of target samples

nRefSamples

public int nRefSamples()

Description copied from interface: Data

Returns the number of reference samples.

Specified by:

nRefSamples in interface Data

Returns:

the number of reference samples

refSamples

public Samples refSamples()

Description copied from interface: Data

Returns the list of reference samples, or null if there are no reference samples.

Specified by:

refSamples in interface Data

Returns:

the list of reference samples, or null if there are no reference samples

nAllSamples

public int nAllSamples()

Description copied from interface: Data

Returns the total number of reference and target samples.

Specified by:

nAllSamples in interface Data

Returns:

the total number of reference and target samples

allSamples

public Samples allSamples()

Description copied from interface: Data

Returns a list of all target and reference samples. Target samples are listed first in the same order as the list returned by this.targetSamples(). Reference samples are listed last in the same order as the list returned by this.refSamples().

Specified by:

allSamples in interface Data

Returns:

a list of all target and reference samples

targGT

public GT targGT()

Description copied from interface: Data

Returns the genotype likelihoods for the target samples restricted to the target data markers in the current window. The returned GL instance will contain no markers if this.advanceWindow() has not yet been invoked.

Specified by:

targGT in interface Data

Returns:

the genotype likelihoods for the target samples restricted to the target data markers in the current window

restrictedRefHapPairs

public java.util.List<HapPair> restrictedRefHapPairs()

Description copied from interface: Data

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 if this.advanceWindow() has not yet been invoked.

Specified by:

restrictedRefHapPairs in interface Data

Returns:

a list of reference haplotype pairs that are restricted to the target data markers

refHapPairs

public java.util.List<HapPair> refHapPairs()

Description copied from interface: Data

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 if this.advanceWindow() has not yet been invoked.

Specified by:

refHapPairs in interface Data

Returns:

a list of the reference haplotype pairs

refGT

public RefGT refGT()

Description copied from interface: Data

Returns the phased, nonmissing reference genotype data for the current window, or null if there are no reference data

Specified by:

refGT in interface Data

Returns:

the reference genotype data for the current window or null if there are no reference data

restrictRefGT

public RefGT restrictRefGT()

Description copied from interface: Data

Returns the phased, nonmissing reference genotype data for the target data markers in the current window. Returns null if there are no reference data

Specified by:

restrictRefGT in interface Data

Returns:

the reference genotype data for the target data markers in the current window or null if there are no reference data

close

public void close()

Description copied from interface: Data

Releases any I/O resources controlled by this object.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface Data

toString

public java.lang.String toString()

Returns a string representation of this. The exact details of the representation are unspecified and subject to change.

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this