Package bref

Class AsIsBref3Writer

  • All Implemented Interfaces:
    BrefWriter, java.io.Closeable, java.lang.AutoCloseable
    public class AsIsBref3Writer
extends java.lang.Object
implements BrefWriter

    Class AsIsBref3Writer writes VCF data with phased, non-missing genotypes to a binary reference format v3 (bref) file. Each record that is written will have the same internal representation (allele-coded or sequence-coded) as the RefGTRec passed to the write() method. 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 AsIsBref3Writer 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_V3
      The initial integer in a bref version 3 file.
      int MAX_SAMPLES  
      static byte SEQ_CODED
      The byte value denoting a sequence coded record

    • Constructor Summary

      Constructors 
      Constructor Description
      AsIsBref3Writer​(java.lang.String program, Samples samples, java.io.File brefFile)
      Constructs a new AsIsBref4Writer 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

    • Field Detail

      • END_OF_DATA

        public static final int END_OF_DATA
        The end of file code for a bref file.
        See Also:
        Constant Field Values

      • END_OF_INDEX

        public 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_V3

        public static final int MAGIC_NUMBER_V3
        The initial integer in a bref version 3 file.
        See Also:
        Constant Field Values

      • SEQ_CODED

        public static final byte SEQ_CODED
        The byte value denoting a sequence coded record
        See Also:
        Constant Field Values

      • ALLELE_CODED

        public static final byte ALLELE_CODED
        The byte value denoting an allele coded record
        See Also:
        Constant Field Values

    • Constructor Detail

      • AsIsBref3Writer

        public AsIsBref3Writer​(java.lang.String program,
                       Samples samples,
                       java.io.File brefFile)
        Constructs a new AsIsBref4Writer for the specified data. The Java virtual machine will exit with an error message if an I/O error occurs during object construction
        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
        brefFile - name of the output binary reference file or null if the output should be directed to standard output
        Throws:
        java.lang.IllegalArgumentException - if { samples.size() > AsIsBref4Writer.MAX_SAMPLES
        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