Class ReadsOnMarkersModel


  • public class ReadsOnMarkersModel
    extends java.lang.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 Detail

      • ReadsOnMarkersModel

        public ReadsOnMarkersModel​(SnpEffectPredictor snpEffectPredictor)
    • Method Detail

      • countBases

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

        public CountByType getCountMarkers()
      • getRawCountBases

        public CountByType getRawCountBases()
      • getRawCountMarkers

        public CountByType getRawCountMarkers()
      • load

        public void load​(java.lang.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​(java.lang.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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object