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