Package org.snpeff.nmer

Class NmerCount

java.lang.Object
org.snpeff.nmer.NmerCount
All Implemented Interfaces:
Serializable
Direct Known Subclasses:
NmerCountWc
public class NmerCount extends Object implements Serializable
Mark if an Nmer has been 'seen' It only count up to 255 (one byte per counter)
Author:
pcingola
See Also:

  • Field Details

    • debug

      public static boolean debug

  • Constructor Details

    • NmerCount

      public NmerCount(int nmerSize)

  • Method Details

    • avg

      public double avg()
      Average number of nmers
      Parameters:
      threshold -
      Returns:

    • count

      public void count(Nmer nmer)
      Count an instance of this Nmer
      Parameters:
      nmer -

    • countLessThan

      public long countLessThan(int threshold)
      Count how many nmers are below a given threshold
      Parameters:
      threshold -
      Returns:

    • get

      protected int get(long key)

    • get

      public int get(Nmer nmer)
      Get kmer count
      Parameters:
      nmer -
      Returns:

    • max

      public long max()
      Max nmer count
      Parameters:
      threshold -
      Returns:

    • max

      public long max(NmerCount nullDistribution)
      Max nmer count
      Parameters:
      threshold -
      Returns:

    • random

      public void random(int iterations)
      Create random sequences and count nmers This is used to create a null distribution
      Parameters:
      iterations -

    • size

      public int size()

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • toStringAll

      public String toStringAll()

    • toStringAll

      public String toStringAll(int minCount)

    • total

      public long total()
      Total number of nmers
      Parameters:
      threshold -
      Returns: