Package org.snpeff.overlap
Class Overlap<S extends BinarySequence>
java.lang.Object
org.snpeff.overlap.Overlap<S>
- Direct Known Subclasses:
OverlapDnaSeq
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 Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionint
int
abstract int
Calculate the best overlap between two sequences
-
Constructor Details
-
Overlap
public Overlap()
-
-
Method Details
-
getBestOffset
public int getBestOffset() -
getBestScore
public int getBestScore() -
overlap
Calculate the best overlap between two sequences- Parameters:
seq1
-seq1
-- Returns:
-