Package org.snpeff.stats

Class ReadsOnMarkersModel

java.lang.Object
org.snpeff.stats.ReadsOnMarkersModel
public class ReadsOnMarkersModel extends Object
Calculate the maximum interval length by type, for all markers in a genome Create a probability model based on binomial ditribution.
Author:
pcingola

  • Constructor Details

  • Method Details

    • countBases

      public void countBases()
      Count bases covered for each marker type

    • getCountBases

      public CountByType getCountBases()

    • getCountMarkers

      public CountByType getCountMarkers()

    • getProb

      public CountByType getProb()

    • getRawCountBases

      public CountByType getRawCountBases()

    • getRawCountMarkers

      public CountByType getRawCountMarkers()

    • load

      public void load(String fileName)
      Load data from a file
      Parameters:
      fileName -

    • randomSampling

      public void randomSampling(int iterations, int readLen, int numReads)
      Sample and calculate the probability of hitting each type of marker (marker.class). Creates 'numReads' reads of size 'readLen' and count how many of them hit each marker type. Iterate 'iterations' times to obtain a distribution.

    • run

      public boolean run()
      Run
      Returns:

    • save

      public void save(String fileName)
      Save model to file
      Parameters:
      fileName -

    • setMarkerTypes

      public void setMarkerTypes(MarkerTypes markerTypes)

    • setNumIterations

      public void setNumIterations(int numIterations)

    • setNumReads

      public void setNumReads(int numReads)

    • setReadLength

      public void setReadLength(int readLength)

    • setSnpEffectPredictor

      public void setSnpEffectPredictor(SnpEffectPredictor snpEffectPredictor)

    • setVerbose

      public void setVerbose(boolean verbose)

    • toString

      public String toString()
      Overrides:
      toString in class Object