Initialize

Algorithm.h

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+// Methods related to alignment and string operations
+#ifndef _LSONG_ALIGNMENT_HEADER
+#define _LSONG_ALIGNMENT_HEADER
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "KmerCode.h"
+#include "SimpleVector.h"
+#include "defs.h"
+
+void ReverseComplement( char *s, int len ) ;
+
+// We had a kmer hit from pa and pb on the two sequences.
+// Then we can decide whether these two sequences are from the strand or not.
+bool IsSameStrand( char *sa, index_t pa, char *sb, index_t pb, int kmerLength ) ;
+
+// Is sequence sa and sb similar and overlapped?
+// The overlapped region are stored in rangeA and rangeB for sequence A, B
+// hits hold the kmer hits offset, a for seqA, b for seqB.
+bool IsOverlap( SimpleVector< struct _pair > &hits, bool sameStrand, int minHitRequired, struct _pair &rangeA, struct _pair &rangeB, SimpleVector< struct _pair > *retLIS ) ;
+
+int GlobalAlignment( char *t, int lent, char *p, int lenp, char *align ) ;
+int GlobalAlignment_classic( char *t, int lent, char *p, int lenp, char *align ) ;
+void VisualizeAlignment( char *t, int lent, char *p, int lenp, char *align ) ;
+#endif