Package bref

Class CompressBref3Writer

java.lang.Object
bref.CompressBref3Writer
All Implemented Interfaces:
BrefWriter, Closeable, AutoCloseable
public class CompressBref3Writer extends 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 Details

    • CompressBref3Writer

      public CompressBref3Writer(String program, Samples samples, int maxNSeq, 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:
      IllegalArgumentException - maxNSeq < 0 || maxNSeq >= Character.MAX_VALUE
      NullPointerException - if program == null || samples == null

  • Method Details

    • 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 AutoCloseable
      Specified by:
      close in interface BrefWriter
      Specified by:
      close in interface Closeable