Class Overlap<S extends BinarySequence>

java.lang.Object
org.snpeff.overlap.Overlap<S>
Direct Known Subclasses:
OverlapDnaSeq

public abstract class Overlap<S extends BinarySequence> extends Object
Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.
Author:
pcingola
  • Constructor Details

    • Overlap

      public Overlap()
  • Method Details

    • getBestOffset

      public int getBestOffset()
    • getBestScore

      public int getBestScore()
    • overlap

      public abstract int overlap(S seq1, S seq2)
      Calculate the best overlap between two sequences
      Parameters:
      seq1 -
      seq1 -
      Returns: