org.utgenome.util.aligner
Class SmithWatermanAligner.Config

java.lang.Object
  org.utgenome.util.aligner.SmithWatermanAligner.Config

Enclosing class:

SmithWatermanAligner

public static class SmithWatermanAligner.Config
extends Object

Field Summary

boolean	BSS_ALIGNMENT for BSS alignment
int	BSS_CT_MISMATCH_PENALTY
int	GAPOPEN_PENALTY
int	MATCH_SCORE
int	MISMATCH_PENALTY

Constructor Summary

SmithWatermanAligner.Config()

Method Summary

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MATCH_SCORE

public int MATCH_SCORE

MISMATCH_PENALTY

public int MISMATCH_PENALTY

GAPOPEN_PENALTY

public int GAPOPEN_PENALTY

BSS_ALIGNMENT

public boolean BSS_ALIGNMENT

for BSS alignment

BSS_CT_MISMATCH_PENALTY

public int BSS_CT_MISMATCH_PENALTY

Constructor Detail

SmithWatermanAligner.Config

public SmithWatermanAligner.Config()