Package bref

Class 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

      All Methods Instance Methods Concrete 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.

      • 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