vcf

Class VcfWindow

java.lang.Object

vcf.VcfWindow

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

public class VcfWindow
extends java.lang.Object
implements java.io.Closeable

Class VcfWindow represents a sliding window of VCF records.

Instances of class VcfWindow are not thread-safe.

Constructor Summary

Constructors

Constructor and Description
VcfWindow(SampleFileIt<? extends VcfEmission> it) Constructs a new VcfWindow instance.

Method Summary

Modifier and Type	Method and Description
VcfEmission[]	advanceWindow(int overlap, int windowSize) Advances the sliding window of VCF records, and returns the advanced window as a VcfEmission[] object.
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.
int	cumMarkerCnt() Returns the number of distinct VCF records in the union of the current window and all previous windows.
java.io.File	file() Returns the file from which VCF records are read, or returns null if the source is standard input.
boolean	lastWindowOnChrom() Returns true if the sliding window of VCF Records is the last window for the chromosome and returns false otherwise.
int	nSamples() Returns the number of samples.
int	overlap() Returns the number of VCF records in the overlap between the current window and the previous window.
Samples	samples() Returns the list of samples.
int	size() Returns the number of VCF records in the current window.
java.lang.String	toString() Returns a string representation of this.

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfWindow

public VcfWindow(SampleFileIt<? extends VcfEmission> it)

Constructs a new VcfWindow instance.

Parameters:

it - an iterator that returns VCF records

Throws:

java.lang.IllegalArgumentException - if it.hasNext() == false

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

java.lang.NullPointerException - if it == null

Method Detail

lastWindowOnChrom

public boolean lastWindowOnChrom()

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

Returns:

true if the sliding window of VCF Records is the last window for the chromosome

canAdvanceWindow

public boolean canAdvanceWindow()

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

Returns:

true if the sliding window of VCF records can advance

advanceWindow

public VcfEmission[] advanceWindow(int overlap,
                                   int windowSize)

Advances the sliding window of VCF records, and returns the advanced window as a VcfEmission[] object. The size of the advanced window and the number of markers of overlap between the marker window immediately before method invocation and the marker window immediately after method invocation may differ from the requested values. If the advanced window size or overlap is less than the requested value, the actual value will be as large as possible. If this.lastWindowOnChrom() == true before method invocation, then there will be no overlap between the advanced window and the previous window.

Parameters:

overlap - the number of markers of overlap

windowSize - the requested number of the markers in the window immediately after the method returns

Returns:

the advanced window of VCF records

Throws:

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

java.lang.IllegalArgumentException - if overlap < 0 || overlap >= windowSize

java.lang.IllegalArgumentException - if overlap > this.size() at the time of method invocation

java.lang.IllegalArgumentException - if overlap > 0 && this.lastWindowOnChromosome() == true

java.lang.IllegalStateException - if this.canAdvanceWindow() == false

file

public java.io.File file()

Returns the file from which VCF records are read, or returns null if the source is standard input.

Returns:

the file from which VCF records are read, or null if the source is standard input

samples

public Samples samples()

Returns the list of samples.

Returns:

the list of samples

nSamples

public int nSamples()

Returns the number of samples.

Returns:

the number of samples

size

public int size()

Returns the number of VCF records in the current window.

Returns:

the number of VCF records in the current window

overlap

public 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

cumMarkerCnt

public int cumMarkerCnt()

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

Returns:

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

close

public void close()

Releases any I/O resources controlled by this object.

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

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