1 #ifndef CODE_ParametersGenome 2 #define CODE_ParametersGenome 3 4 #include "IncludeDefine.h" 5 6 class Parameters; 7 8 class ParametersGenome {//"constant" genome parameters - user input 9 public: 10 string gDir; 11 string gLoad; 12 13 uint32 gType;//type code 14 string gTypeString; 15 16 vector <string> gFastaFiles; 17 vector <string> gChainFiles; 18 //string gConsensusFile; DEPRECATED 19 20 struct { 21 int32 type; 22 string typeString; 23 string vcfFile; 24 vector<string> output; //which output to transform 25 bool outYes, outSAM, outSJ; 26 } transform; 27 28 uint gSAindexNbases;//length of the SA pre-index strings 29 uint gChrBinNbits; 30 uint gSAsparseD;//SA sparsity 31 uint gSuffixLengthMax;//maximum length of the suffixes, has to be longer than read length 32 vector <uint> gFileSizes;//size of the genome files 33 34 vector <string> sjdbFileChrStartEnd; 35 string sjdbGTFfile; 36 string sjdbGTFchrPrefix; 37 38 string sjdbGTFfeatureExon; 39 string sjdbGTFtagExonParentTranscript; 40 string sjdbGTFtagExonParentGene; 41 vector<string> sjdbGTFtagExonParentGeneName; 42 vector<string> sjdbGTFtagExonParentGeneType; 43 44 string sjdbInsertSave; 45 uint sjdbOverhang; 46 int sjdbOverhang_par; 47 int sjdbScore; 48 49 void initialize(Parameters *Pin); 50 51 private: 52 Parameters *pP; 53 54 }; 55 56 #endif 57