Class VcfGenotype

Method Details

• add

  public void add(String name, String value)

  Add a name=value pair WARNING: This method does NOT change the FORMAT field. Use VcfEntry.addFormat() method

• depth

  public int depth()

  Depth of coverage

  Returns:

  -1 if not found

• get

  public String get(String fieldName)

  Get a genotype field

• getGenotype

  public int[] getGenotype()

  Get genotype numbers as an array E.g. '0/1' -> {0, 1} WARNING: If the genotype is missing, the numeric value is '-1'. E.g.: './.' -> {-1, -1}

  Returns:

• getGenotype

  public String getGenotype(int idx)

  Get genotype string by index WARNING: If the genotype is missing, it returns an empty string. E.g.: './.' -> getGenotype(0) = ""

  Returns:

• getGenotypeCode

  public int getGenotypeCode()

  Return as a genotype SNP code: -1: if missing data of more than one ALT 0: if aa (0/0) 1: if Aa (0/1 or 1/0) 2: if AA (1/1) WARNING: In multi-allelic case, any non-ref is treated as ALT

  Returns:

• getGenotypeCodeIgnoreMissing

  public int getGenotypeCodeIgnoreMissing()

  Return as a genotype SNP code: 0: if aa (0/0) or any missing value 1: if Aa (0/1 or 1/0) 2: if AA (1/1)

  Returns:

• getGenotypeStr

  public String getGenotypeStr()

  Return genotypes as string (e.g. "A/C")

  Returns:

• getVcfEntry

  public VcfEntry getVcfEntry()

• isHeterozygous

  public boolean isHeterozygous()

  Is the most likely genotype heterozygous?

  Returns:

• isHomozygous

  public boolean isHomozygous()

  Is this genotype homozygous? (either REF or ALT)

• isHomozygousAlt

  public boolean isHomozygousAlt()

  Is this genotype homozygous ALT?

• isMissing

  public boolean isMissing()

  Is genotpye missing (e.g. "GT=./.")

  Returns:

• isPhased

  public boolean isPhased()

• isRef

  public boolean isRef()

  Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)

• isVariant

  public boolean isVariant()

  Is any genotype different than REF? Note: This is calculated for the most likely genotype (GT field)

• plodity

  public int plodity()

  Genotype plodity (i.e. how many copies of the chromosome does it have)

• set

  public void set(String gtFieldName, String gtValue)

  Set a genotype field value

• setGenotype

  public void setGenotype(String gtValue)

  Set genotype value

• toString

  public String toString()

  Overrides:

  toString in class Object