1 #ifndef CODE_SuffixArrayFuns
2 #define CODE_SuffixArrayFuns
3 
4 #include "IncludeDefine.h"
5 #include "Parameters.h"
6 #include "PackedArray.h"
7 #include "Genome.h"
8 
9 uint medianUint2(uint, uint);
10 uint compareSeqToGenome(Genome &mapGen, char** s2, uint S, uint N, uint L, uint iSA, bool dirR, bool& comparRes);
11 uint findMultRange(Genome &mapGen, uint i3, uint L3, uint i1, uint L1, uint i1a, uint L1a, uint i1b, uint L1b, char** s, bool dirR, uint S);
12 uint maxMappableLength(Genome &mapGen, char** s, uint S, uint N, uint i1, uint i2, bool dirR, uint& L, uint* indStartEnd);
13 void writePacked(Genome &mapGen, char* a, uint jj, uint x);
14 uint readPacked(Genome &mapGen, char* a, uint jj);
15 uint suffixArraySearch1(Genome &mapGen, char** s2, uint S, uint N, uint64 gInsert, bool dirR, uint i1, uint i2, uint L);
16 int64 funCalcSAi(char *G, uint iL);
17 uint funCalcSAiFromSA(char* gSeq, PackedArray& gSA, Genome &mapGen, uint iSA, int L, int & iL4);
18 #endif
19