Package bref

Class SeqCoder3

java.lang.Object
bref.SeqCoder3
public class SeqCoder3 extends Object

Class SeqCoder3 compresses a sequence of allele-coded RefGTRec objects. The class is designed for use with bref v3 format. Compression is performed by storing the list of distinct allele sequences and the allele sequence carried by each haplotype.

Class SeqCoder3 is not thread-safe.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    static final float
    COMPRESS_FREQ_THRESHOLD
    The major allele frequency threshold for allele coding.
    static final int
    MAX_NALLELES
    The maximum number of alleles are that permitted in order for the add() method to return true

  • Constructor Summary

    Constructors
    Constructor
    Description
    SeqCoder3(Samples samples)
    Constructs a new SeqCoder3 for the specified samples.
    SeqCoder3(Samples samples, int maxNSeq)
    Constructs a new SeqCoder3 for the specified samples.

  • Method Summary

    Modifier and Type
    Method
    Description
    boolean
    add(RefGTRec rec)
    Attempts to add the specified RefGTRec object to the list of compressed RefGTRec objects, and returns true if the RefGTRec object was added.
    static int
    defaultMaxNSeq(int nSamples)
    Returns the default maximum number of sequences for the specified number of samples.
    List<RefGTRec>
    getCompressedList()
    Returns and clears the stored list of compressed RefGTRec objects.
    int
    maxNSeq()
    Returns the maximum number of distinct allele sequences.
    int
    nRecs()
    Returns the number of compressed RefGTRec objects.
    Samples
    samples()
    Returns the list of samples whose phased genotype data will be compressed.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • MAX_NALLELES

      public static final int MAX_NALLELES
      The maximum number of alleles are that permitted in order for the add() method to return true
      See Also:

    • COMPRESS_FREQ_THRESHOLD

      public static final float COMPRESS_FREQ_THRESHOLD
      The major allele frequency threshold for allele coding. Sequence coding should only be applied if the major allele frequency less than or equal to this threshold.
      See Also:

  • Constructor Details

    • SeqCoder3

      public SeqCoder3(Samples samples)
      Constructs a new SeqCoder3 for the specified samples.
      Parameters:
      samples - the list of samples whose data will be compressed
      Throws:
      NullPointerException - if samples == null

    • SeqCoder3

      public SeqCoder3(Samples samples, int maxNSeq)
      Constructs a new SeqCoder3 for the specified samples.
      Parameters:
      samples - the list of samples whose data will be compressed
      maxNSeq - the maximum number of distinct allele sequences permitted if the add() method returns true
      Throws:
      NullPointerException - if samples == null
      IllegalArgumentException - maxNSeq < 0 || maxNSeq >= Character.MAX_VALUE

  • Method Details

    • defaultMaxNSeq

      public static int defaultMaxNSeq(int nSamples)
      Returns the default maximum number of sequences for the specified number of samples. The default value is equal to (int) Math.min((long) Math.pow(2, 2*Math.log10(size) + 1), Character.MAX_VALUE)
      Parameters:
      nSamples - the number of samples
      Returns:
      the default maximum number of sequences for the specified number of samples
      Throws:
      IllegalArgumentException - if size < 1

    • samples

      public Samples samples()
      Returns the list of samples whose phased genotype data will be compressed.
      Returns:
      the list of samples whose phased genotype data will be compressed

    • nRecs

      public int nRecs()
      Returns the number of compressed RefGTRec objects.
      Returns:
      the number of compressed RefGTRec objects

    • maxNSeq

      public int maxNSeq()
      Returns the maximum number of distinct allele sequences.
      Returns:
      the maximum number of distinct allele sequences

    • add

      public boolean add(RefGTRec rec)
      Attempts to add the specified RefGTRec object to the list of compressed RefGTRec objects, and returns true if the RefGTRec object was added.
      Parameters:
      rec - reference genotypes for a marker
      Returns:
      true if the specified RefGTRec object was added to the list of compressed markers
      Throws:
      IllegalArgumentException - if rec.samples().equals(this.samples()) == false
      IllegalArgumentException - if rec.isAlleleCoded() == false
      NullPointerException - if rec == null

    • getCompressedList

      public List<RefGTRec> getCompressedList()
      Returns and clears the stored list of compressed RefGTRec objects.
      Returns:
      the list of compressed RefGTRec objects