Class Coverage

  • All Implemented Interfaces:
    java.io.Serializable

    public class Coverage
    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
      Coverage()  
    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double avgCoverage​(Marker m)
      Calculate average coverage per base
      static Coverage calculateFromSam​(java.lang.String samFile, boolean verbose)
      Calculate coverage from a SAM file
      long coverage​(Marker m)
      Calculate total coverage per base
      void createChr​(java.lang.String chr, int len)
      Create new chromosome coverage
      CoverageChr get​(java.lang.String chr)  
      void inc​(java.lang.String chr, 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

      • Coverage

        public Coverage()
    • Method Detail

      • calculateFromSam

        public static Coverage calculateFromSam​(java.lang.String samFile,
                                                boolean verbose)
        Calculate coverage from a SAM file
        Parameters:
        samFile -
        verbose -
        Returns:
      • avgCoverage

        public double avgCoverage​(Marker m)
        Calculate average coverage per base
        Parameters:
        m - : A marker interval
        Returns:
      • coverage

        public long coverage​(Marker m)
        Calculate total coverage per base
        Parameters:
        m - : A marker interval
        Returns:
      • createChr

        public void createChr​(java.lang.String chr,
                              int len)
        Create new chromosome coverage
        Parameters:
        chr -
        len -
      • get

        public CoverageChr get​(java.lang.String chr)
      • inc

        public void inc​(java.lang.String chr,
                        int start,
                        int end)
        Increment a region
        Parameters:
        start -
        end -
      • toString

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