Package org.snpeff.coverage

Class CountFragments

java.lang.Object
org.snpeff.coverage.CountFragments
All Implemented Interfaces:
Serializable
public class CountFragments extends Object implements Serializable
Base by base coverage (one chromsome)
Author:
pcingola
See Also:

  • Constructor Details

    • CountFragments

      public CountFragments()

  • Method Details

    • calculateFromSam

      public static CountFragments calculateFromSam(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(String chr, int len)
      Create new chromosome coverage
      Parameters:
      chr -
      len -

    • get

      public CoverageChr get(String chr)

    • inc

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

    • toString

      public String toString()
      Overrides:
      toString in class Object