Package org.snpeff.overlap
Class Overlap<S extends BinarySequence>
- java.lang.Object
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- org.snpeff.overlap.Overlap<S>
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- Direct Known Subclasses:
OverlapDnaSeq
public abstract class Overlap<S extends BinarySequence> extends java.lang.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
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Constructor Summary
Constructors Constructor Description Overlap()
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Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description int
getBestOffset()
int
getBestScore()
abstract int
overlap(S seq1, S seq2)
Calculate the best overlap between two sequences
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