Package bref

Class CompressBref3Writer

java.lang.Object

bref.CompressBref3Writer

All Implemented Interfaces:

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

public class CompressBref3Writer
extends java.lang.Object
implements BrefWriter

Class CompressBref3Writer writes phased, non-missing genotypes to a binary reference format v3 (bref) file. The close() method must be called after the last invocation of the write() method in order to ensure that all buffered data is written to the output binary reference file.

Instances of class CompressBrerf3Writer are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
CompressBref3Writer(java.lang.String program, Samples samples, int maxNSeq, java.io.File brefFile)	Constructs a new CompressBref3fWriter 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

Constructor Detail

CompressBref3Writer

public CompressBref3Writer(java.lang.String program,
                           Samples samples,
                           int maxNSeq,
                           java.io.File brefFile)

Constructs a new CompressBref3fWriter for the specified data. The Java virtual machine will exit with an error message if an I/O error occurs.

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

maxNSeq - the maximum number of distinct allele sequences in a compressed block

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

Throws:

java.lang.IllegalArgumentException - maxNSeq < 0 || maxNSeq >= Chracter.MAX_VALUE

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