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 | Description |
---|---|
CompressBref3Writer(java.lang.String program,
Samples samples,
int maxNSeq,
java.io.File brefFile) |
Constructs a new
CompressBref3fWriter for the specified data. |
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.
|
public CompressBref3Writer(java.lang.String program, Samples samples, int maxNSeq, java.io.File brefFile)
CompressBref3fWriter
for the specified data.
The Java virtual machine will exit with an error message if an I/O
error occurs.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 formatmaxNSeq
- the maximum number of distinct allele sequences
in a compressed blockbrefFile
- name of the output binary reference file or
null
if the output should be directed to standard outputjava.lang.IllegalArgumentException
- maxNSeq < 0 || maxNSeq >= Chracter.MAX_VALUE
java.lang.NullPointerException
- if program == null || samples == null
public Samples samples()
BrefWriter
samples
in interface BrefWriter
public void write(RefGTRec rec)
BrefWriter
this.close()
has previously been invoked, or if
rec.samples().equals(this.samples()) == false
.write
in interface BrefWriter
rec
- phased genotype datapublic void close()
BrefWriter
BrefWriter
. The Java virtual machine will exit
with an error message if an I/O error occurs during method execution.close
in interface java.lang.AutoCloseable
close
in interface BrefWriter
close
in interface java.io.Closeable