Package gorsat.gtgen

Class GTGen

java.lang.Object
gorsat.gtgen.GTGen
public class GTGen extends Object
A class for running simple joint variant calling.

  • Constructor Summary

    Constructors
    Constructor
    Description
    GTGen(double e, int n)
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    addData(int sampleIdx, double pAA, double pAB, double pBB)
     
    void
    addData(int sampleIdx, int call, int depth)
     
    double
    get_pAB()
     
    double
    get_pBB()
     
    double
    getAF()
     
    int
    getAn()
     
    int
    getNumberOfSamples()
     
    double
    getPriorAf()
     
    int
    getPriorAn()
     
    boolean
    hasCoverage(int idx)
     
    boolean
    impute(double[] gts, double tol, int maxIt)
    Estimates the allele frequency of the cohort and then computes the genotype probabilities.
    void
    reset()
    Resets the object.
    void
    setAF(double af)
    Sets the allele frequency which we are assuming to have been used when computing the given triplets.
    void
    setAFsinglePriors(double fpab, double fpbb)
     
    void
    setPrior(double pab, double pbb, int m)
    Indicates that our n samples are a part of a bigger cohort of m + n samples, and for the m ones, excluding ours, the estimated allele frequency is af.
    void
    setPrior(double af, int m)
     

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • GTGen

      public GTGen(double e, int n)
      Parameters:
      e - The estimated error frequency.
      n - The number of samples.

  • Method Details

    • reset

      public void reset()
      Resets the object. Can be used as new.

    • getNumberOfSamples

      public int getNumberOfSamples()

    • getPriorAf

      public double getPriorAf()

    • getPriorAn

      public int getPriorAn()

    • setAF

      public void setAF(double af)
      Sets the allele frequency which we are assuming to have been used when computing the given triplets.

    • setAFsinglePriors

      public void setAFsinglePriors(double fpab, double fpbb)

    • getAF

      public double getAF()

    • get_pAB

      public double get_pAB()

    • get_pBB

      public double get_pBB()

    • hasCoverage

      public boolean hasCoverage(int idx)
      Returns:
      Returns whether there is some data for sample with index idx.

    • getAn

      public int getAn()
      Returns:
      Returns the number of samples which have coverage.

    • setPrior

      public void setPrior(double pab, double pbb, int m)
      Indicates that our n samples are a part of a bigger cohort of m + n samples, and for the m ones, excluding ours, the estimated allele frequency is af. The resulting allele frequency will be the same as if we had called them all together at first.

    • setPrior

      public void setPrior(double af, int m)

    • addData

      public void addData(int sampleIdx, double pAA, double pAB, double pBB)

    • addData

      public void addData(int sampleIdx, int call, int depth)

    • impute

      public boolean impute(double[] gts, double tol, int maxIt)
      Estimates the allele frequency of the cohort and then computes the genotype probabilities.
      Parameters:
      gts - An array of size 3*n.
      tol - The tolerance in the allele frequency estimate.
      maxIt - The maximum number of iterations.
      Returns:
      Whether we managed to estimate the allele frequency up to the desired accuracy.