Package bref

Class AsIsBref3Writer

java.lang.Object

bref.AsIsBref3Writer

All Implemented Interfaces:

BrefWriter, java.io.Closeable, java.lang.AutoCloseable

public class AsIsBref3Writer
extends java.lang.Object
implements BrefWriter

Class AsIsBref3Writer writes VCF data with phased, non-missing genotypes to a binary reference format v3 (bref) file. Each record that is written will have the same internal representation (allele-coded or sequence-coded) as the RefGTRec passed to the write() method. The close() method must be called after the last invocation of the write() method in order to ensure that any buffered data are written to the output binary reference file.

Instances of class AsIsBref3Writer are not thread-safe.

Field Summary

Fields

Modifier and Type	Field	Description
static byte	ALLELE_CODED	The byte value denoting an allele coded record
static int	END_OF_DATA	The end of file code for a bref file.
static long	END_OF_INDEX	The integer denoting denoting the end of the index in a bref file
static int	MAGIC_NUMBER_V3	The initial integer in a bref version 3 file.
int	MAX_SAMPLES
static byte	SEQ_CODED	The byte value denoting a sequence coded record

Constructor Summary

Constructors

Constructor	Description
AsIsBref3Writer(java.lang.String program, Samples samples, java.io.File brefFile)	Constructs a new AsIsBref4Writer for the specified data.

Method Summary

Modifier and Type	Method	Description
void	close()	Flushes any buffered output and releases any system resources that are held by this BrefWriter.
Samples	samples()	Returns the list of samples.
void	write(RefGTRec rec)	Writes the specified phased genotype data in binary reference format.

Methods inherited from class java.lang.Object

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

Field Detail

END_OF_DATA

public static final int END_OF_DATA

The end of file code for a bref file.

See Also:

Constant Field Values

END_OF_INDEX

public static final long END_OF_INDEX

The integer denoting denoting the end of the index in a bref file

See Also:

Constant Field Values

MAGIC_NUMBER_V3

public static final int MAGIC_NUMBER_V3

The initial integer in a bref version 3 file.

See Also:

Constant Field Values

SEQ_CODED

public static final byte SEQ_CODED

The byte value denoting a sequence coded record

See Also:

Constant Field Values

ALLELE_CODED

public static final byte ALLELE_CODED

The byte value denoting an allele coded record

See Also:

Constant Field Values

MAX_SAMPLES

public final int MAX_SAMPLES

See Also:

Constant Field Values

Constructor Detail

AsIsBref3Writer

public AsIsBref3Writer(java.lang.String program,
                       Samples samples,
                       java.io.File brefFile)

Constructs a new AsIsBref4Writer for the specified data. The Java virtual machine will exit with an error message if an I/O error occurs during object construction

Parameters:

program - the name of the program which is creating the binary reference file.

samples - the list of samples whose genotype data will be written in binary reference format

brefFile - name of the output binary reference file or null if the output should be directed to standard output

Throws:

java.lang.IllegalArgumentException - if { samples.nSamples() > AsIsBref4Writer.MAX_SAMPLES

java.lang.NullPointerException - if program == null || samples == null

Method Detail

samples

public Samples samples()

Description copied from interface: BrefWriter

Returns the list of samples.

Specified by:

samples in interface BrefWriter

Returns:

the list of samples

write

public void write(RefGTRec rec)

Description copied from interface: BrefWriter

Writes the specified phased genotype data in binary reference format. The Java virtual machine will exit with an error message if an I/O error occurs during method execution, if this.close() has previously been invoked, or if rec.samples().equals(this.samples()) == false.

Specified by:

write in interface BrefWriter

Parameters:

rec - phased genotype data

close

public void close()

Description copied from interface: BrefWriter

Flushes any buffered output and releases any system resources that are held by this BrefWriter. The Java virtual machine will exit with an error message if an I/O error occurs during method execution.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface BrefWriter

Specified by:

close in interface java.io.Closeable