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