@ Override public SWNativeAlignerResult align ( byte [ ] refArray , byte [ ] altArray , SWParameters parameters , SWOverhangStrategy overhangStrategy ) { int intStrategy = getStrategy ( overhangStrategy ) ; byte [ ] cigar = new byte [ 2 * Integer . max ( refArray . length , altArray . length ) ] ; int offset = alignNative ( refArray , altArray , cigar , parameters . getMatchValue ( ) , parameters . getMismatchPenalty ( ) , parameters . getGapOpenPenalty ( ) , parameters . getGapExtendPenalty ( ) , intStrategy ) ; return new SWNativeAlignerResult ( new String ( cigar ) . trim ( ) , offset ) ; }
Implements the native implementation of SmithWaterman and returns the Cigar String and alignment_offset