Class VcfRecGTParser.HapListRep

Method Details

• nonmajorAlleleCnt

  public int nonmajorAlleleCnt()

  Returns the non-major allele count.

  Returns:

  the non-major allele count

• missingSamples

  public int[] missingSamples()

  Returns a list of samples with missing indices

  Returns:

  a list of samples with missing indices

• majorAllele

  public int majorAllele()

  Returns the major allele. The major allele is the allele with largest number of copies. If there are multiple major alleles the major allele with smallest index is returned.

  Returns:

  the major allele

• hapLists

  public int[][] hapLists(boolean setMajorToNull)

  Returns an array of length this.marker().nAlleles() that contains lists of haplotypes carrying each allele. The increasing list of haplotype indices carrying non-major allele j is stored in the j-th element of the returned array. if (@code setMajorToNull == true} then element of the returned array corresponding to this.majorAllele() will be null

  Parameters:

  setMajorToNull - true if the element of the returned array corresponding to this.majorAllele() will be null

  Returns:

  list of haplotypes carrying each allele.

• marker

  public Marker marker()

  Returns the marker.

  Returns:

  the marker

• samples

  public Samples samples()

  Returns the samples.

  Returns:

  the samples

• isPhased

  public boolean isPhased()

  Returns true if all genotypes are phased and there are no missing alleles, and returns false otherwise.

  Returns:

  true if all genotypes are phased and nonomissing