1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
|
#ifndef ASSEMBLY_OPTIONS_H
#define ASSEMBLY_OPTIONS_H 1
#include <string>
#include <vector>
namespace opt {
extern unsigned kmerSize;
extern unsigned singleKmerSize;
extern unsigned kMin;
extern unsigned kMax;
extern unsigned kStep;
extern unsigned erode;
extern unsigned erodeStrand;
extern unsigned trimLen;
extern float coverage;
extern unsigned kc;
extern unsigned bubbleLen;
extern unsigned ss;
extern bool maskCov;
extern std::string coverageHistPath;
extern std::string contigsPath;
extern std::string contigsTempPath;
extern std::string graphPath;
extern std::string snpPath;
extern std::vector<std::string> inFiles;
extern std::string db;
void parse(int argc, char* const* argv);
extern std::string assemblyCmd;
std::vector<std::string> getMetaValue();
int getVvalue();
std::string getUvalue();
std::string getCommand();
}
#endif
|
