Package org.snpeff.coverage

Class CountFragments

  • All Implemented Interfaces:
    java.io.Serializable
    public class CountFragments
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
      CountFragments()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      double avgCoverage​(Marker m)
      Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)
      static CountFragments calculateFromSam​(java.lang.String samFile, boolean verbose)
      Calculate coverage from a SAM file
      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

      • CountFragments

        public CountFragments()

    • Method Detail

      • calculateFromSam

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

      • avgCoverage

        public double avgCoverage​(Marker m)
        Calculate Fragments Per Kilobase of exon per Million fragments mapped (FPKM)
        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