BrefWriter

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Implementing Classes:

AsIsBref3Writer, CompressBref3Writer
```
public interface BrefWriter
extends java.io.Closeable
```
Interface BrefWrites writes phased, non-missing genotypes to a binary reference format (bref) file. 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 BrefWriter 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_V2`	The initial integer in a bref version 2 file.
`static int`	`MAGIC_NUMBER_V3`	The initial integer in a bref version 3 file.
`static byte`	`SEQ_CODED`	The byte value denoting a sequence coded record

Method Summary

All Methods Instance Methods Abstract Methods
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.

- Field Detail
  - END_OF_DATA
```
static final int END_OF_DATA
```
    The end of file code for a bref file.
    
    See Also:
    
    Constant Field Values
  - END_OF_INDEX
```
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_V2
```
static final int MAGIC_NUMBER_V2
```
    The initial integer in a bref version 2 file.
    
    See Also:
    
    Constant Field Values
  - MAGIC_NUMBER_V3
```
static final int MAGIC_NUMBER_V3
```
    The initial integer in a bref version 3 file.
    
    See Also:
    
    Constant Field Values
  - SEQ_CODED
```
static final byte SEQ_CODED
```
    The byte value denoting a sequence coded record
    
    See Also:
    
    Constant Field Values
  - ALLELE_CODED
```
static final byte ALLELE_CODED
```
    The byte value denoting an allele coded record
    
    See Also:
    
    Constant Field Values
- Method Detail
  - samples
```
Samples samples()
```
    Returns the list of samples.
    
    Returns:
    
    the list of samples
  - write
```
void write(RefGTRec rec)
```
    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.
    
    Parameters:
    
    rec - phased genotype data
    
    Throws:
    
    java.lang.NullPointerException - if rec == null
  - close
```
void close()
```
    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 java.io.Closeable

Interface BrefWriter

Field Summary

Method Summary

Field Detail

END_OF_DATA

END_OF_INDEX

MAGIC_NUMBER_V2

MAGIC_NUMBER_V3

SEQ_CODED

ALLELE_CODED

Method Detail

samples

write

close