vcf

Class RestrictedVcfWindow

java.lang.Object

vcf.RestrictedVcfWindow

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable

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

Class RestrictedVcfWindow represents a sliding window of VCF records.

Instances of class RestrictedVcfWindow are not thread.safe.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
VcfEmission[]	advanceWindow(Markers nextMarkers) Advances the sliding marker window, and returns the advanced window as a VcfEmission[] object.
void	close() Releases any I/O resources controlled by this object.
int	cumMarkerCnt() Returns the number of 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.
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.
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

RestrictedVcfWindow

public RestrictedVcfWindow(SampleFileIt<? extends VcfEmission> it)

Construct a new RestrictedVcfWindow 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

advanceWindow

public VcfEmission[] advanceWindow(Markers nextMarkers)

Advances the sliding marker window, and returns the advanced window as a VcfEmission[] object. The returned array will have length markers.nMarkers(). Markers not found in the data source will have null entries in the returned array.

Parameters:

nextMarkers - the set of markers in the advanced window

Returns:

the advanced marker window

Throws:

java.lang.IllegalArgumentException - if markers.nMarkers() == 0

java.lang.IllegalArgumentException - if any two of the specified markers are on different chromosomes

java.lang.IllegalArgumentException - if specified markers are inconsistent with a sliding marker window

java.lang.IllegalArgumentException - if the specified markers do not advance the current marker window

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

java.lang.IllegalArgumentException - if the input data does not contain any of the specified markers

java.lang.NullPointerException - if nextMarkers == null

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

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

Returns:

the number of 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