vcf

Class VcfIt<E extends MarkerContainer>

java.lang.Object

vcf.VcfIt<E>

Type Parameters:

E - the type parameter

All Implemented Interfaces:

FileIt<E>, SampleFileIt<E>, java.io.Closeable, java.lang.AutoCloseable, java.util.Iterator<E>

public class VcfIt<E extends MarkerContainer>
extends java.lang.Object
implements SampleFileIt<E>

Class VcfIt represents an iterator whose next() method returns an object storing data from a VCF record.

Instances of class VcfIt are not thread-safe.

Methods of this class will terminate the Java Virtual Machine with an error message if an I/O error or file format error is detected.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEFAULT_BUFFER_SIZE The default number of VCF records stored in a buffer, which is 1000.
static java.util.function.BiFunction<VcfHeader,java.lang.String,VcfEmission>	toBitSetGT A function mapping a string VCF record with GT format fields to a VcfEmission object.
static java.util.function.BiFunction<VcfHeader,java.lang.String,VcfRecord>	toGLRec A function mapping a string VCF record with GL format fields to a VcfRecord object.
static java.util.function.BiFunction<VcfHeader,java.lang.String,VcfRecord>	toGTGLRec A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.

Method Summary

Modifier and Type	Method and Description
void	close() Terminates the iteration and releases any system resources that are held by this object.
static <R extends VcfEmission> VcfIt<R>	create(FileIt<java.lang.String> strIt, java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper) Create and returns a new VcfIt instance from the specified objects.
static <R extends VcfEmission> VcfIt<R>	create(FileIt<java.lang.String> strIt, Filter<java.lang.String> sampleFilter, java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper) Create and returns a new VcfIt instance from the specified objects.
static <R extends VcfEmission> VcfIt<R>	create(FileIt<java.lang.String> strIt, Filter<java.lang.String> sampleFilter, Filter<Marker> markerFilter, java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper) Create and returns a new VcfIt instance from the specified objects.
static <R extends VcfEmission> VcfIt<R>	create(FileIt<java.lang.String> strIt, Filter<java.lang.String> sampleFilter, Filter<Marker> markerFilter, java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper, int bufferSize) Create and returns a new VcfIt instance from the specified objects.
java.io.File	file() Returns the file from which the data are read, or null if the data are read from standard input or are computed data.
boolean	hasNext() Returns true if the iteration has more elements, and returns false otherwise.
E	next() Returns the next element in the iteration.
void	remove() The remove method is not supported by this iterator.
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

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

DEFAULT_BUFFER_SIZE

public static final int DEFAULT_BUFFER_SIZE

The default number of VCF records stored in a buffer, which is 1000.

See Also:

Constant Field Values

toGTGLRec

public static final java.util.function.BiFunction<VcfHeader,java.lang.String,VcfRecord> toGTGLRec

A function mapping a string VCF record with GT or GL format fields to a VcfRecord object.

toGLRec

public static final java.util.function.BiFunction<VcfHeader,java.lang.String,VcfRecord> toGLRec

A function mapping a string VCF record with GL format fields to a VcfRecord object.

toBitSetGT

public static final java.util.function.BiFunction<VcfHeader,java.lang.String,VcfEmission> toBitSetGT

A function mapping a string VCF record with GT format fields to a VcfEmission object.

Method Detail

create

public static <R extends VcfEmission> VcfIt<R> create(FileIt<java.lang.String> strIt,
                                                      java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper)

Create and returns a new VcfIt instance from the specified objects.

Type Parameters:

R - the type returned by the returned VcfIt

Parameters:

strIt - an iterator that returns lines of a VCF file

recMapper - a function mapping string VCF records to VcfEmission objects

Returns:

a new VcfIt instance

Throws:

java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt

java.lang.NullPointerException - if strIt == null || recMapper == null

create

public static <R extends VcfEmission> VcfIt<R> create(FileIt<java.lang.String> strIt,
                                                      Filter<java.lang.String> sampleFilter,
                                                      java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper)

Create and returns a new VcfIt instance from the specified objects.

Type Parameters:

R - the type returned by the returned VcfIt

Parameters:

strIt - an iterator that returns lines of a VCF file

sampleFilter - a sample filter or null

recMapper - a function mapping string VCF records to VcfEmission objects

Returns:

a new VcfIt instance

Throws:

java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt

java.lang.NullPointerException - if strIt == null || recMapper == null

create

public static <R extends VcfEmission> VcfIt<R> create(FileIt<java.lang.String> strIt,
                                                      Filter<java.lang.String> sampleFilter,
                                                      Filter<Marker> markerFilter,
                                                      java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper)

Create and returns a new VcfIt instance from the specified objects.

Type Parameters:

R - the type returned by the returned VcfIt

Parameters:

strIt - an iterator that returns lines of a VCF file

sampleFilter - a sample filter or null

markerFilter - a marker filter or null

recMapper - a function mapping string VCF records to VcfEmission objects

Returns:

a new VcfIt instance

Throws:

java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt

java.lang.NullPointerException - if strIt == null || recMapper == null

create

public static <R extends VcfEmission> VcfIt<R> create(FileIt<java.lang.String> strIt,
                                                      Filter<java.lang.String> sampleFilter,
                                                      Filter<Marker> markerFilter,
                                                      java.util.function.BiFunction<VcfHeader,java.lang.String,R> recMapper,
                                                      int bufferSize)

Create and returns a new VcfIt instance from the specified objects.

Type Parameters:

R - the type returned by the returned VcfIt

Parameters:

strIt - an iterator that returns lines of a VCF file

sampleFilter - a sample filter or null

markerFilter - a marker filter or null

recMapper - a function mapping string VCF records to VcfEmission objects

bufferSize - the buffer size

Returns:

a new VcfIt instance

Throws:

java.lang.IllegalArgumentException - if a format error is detected in a line of a VCF file returned by strIt

java.lang.IllegalArgumentException - if bufferSize < 1

java.lang.NullPointerException - if strIt == null || recMapper == null

close

public void close()

Description copied from interface: FileIt

Terminates the iteration and releases any system resources that are held by this object. After invoking close, further invocations of close() have no effect.

Specified by:

close in interface FileIt<E extends MarkerContainer>

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

hasNext

public boolean hasNext()

Returns true if the iteration has more elements, and returns false otherwise.

Specified by:

hasNext in interface java.util.Iterator<E extends MarkerContainer>

Returns:

true if the iteration has more elements

next

public E next()

Returns the next element in the iteration.

Specified by:

next in interface java.util.Iterator<E extends MarkerContainer>

Returns:

the next element in the iteration

Throws:

java.util.NoSuchElementException - if the iteration has no more elements.

remove

public void remove()

The remove method is not supported by this iterator.

Specified by:

remove in interface java.util.Iterator<E extends MarkerContainer>

Throws:

java.lang.UnsupportedOperationException - if this method is invoked

file

public java.io.File file()

Description copied from interface: FileIt

Returns the file from which the data are read, or null if the data are read from standard input or are computed data.

Specified by:

file in interface FileIt<E extends MarkerContainer>

Returns:

the file from which the data are read, or null if the data are read from standard input or are computed data

samples

public Samples samples()

Description copied from interface: SampleFileIt

Returns the list of samples.

Specified by:

samples in interface SampleFileIt<E extends MarkerContainer>

Returns:

the list of samples

toString

public java.lang.String toString()

Description copied from interface: FileIt

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

Specified by:

toString in interface FileIt<E extends MarkerContainer>

Overrides:

toString in class java.lang.Object

Returns:

a string representation of this