Package org.snpeff.coverage

Class CoverageChr

  • All Implemented Interfaces:
    java.io.Serializable
    public class CoverageChr
extends java.lang.Object
implements java.io.Serializable
    Base by base coverage (one chromsome)
    Author:
    pcingola
    See Also:
    Serialized Form

    • Constructor Summary

      Constructors 
      Constructor Description
      CoverageChr​(int len)  

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double avgCoverage​(int start, int end)
      Calculate Coverage per base
      long coverage​(int start, int end)
      Calculate Coverage per base
      short[] getCount()  
      void inc​(int start, int end)
      Increment a region
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • CoverageChr

        public CoverageChr​(int len)

    • Method Detail

      • avgCoverage

        public double avgCoverage​(int start,
                          int end)
        Calculate Coverage per base
        Returns:
        Average coverage per base

      • coverage

        public long coverage​(int start,
                     int end)
        Calculate Coverage per base
        Returns:
        Average coverage per base

      • getCount

        public short[] getCount()

      • inc

        public void inc​(int start,
                int end)
        Increment a region
        Parameters:
        start -
        end -

      • toString

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