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
|
#ifndef _BLASR_ANCHOR_PARAMETERS_HPP_
#define _BLASR_ANCHOR_PARAMETERS_HPP_
#include <fstream>
#include <iostream>
#include <pbdata/DNASequence.hpp>
#include <pbdata/qvs/QualityValue.hpp>
class AnchorParameters
{
public:
QualityValue branchQualityThreshold;
DNALength minMatchLength;
int maxMatchScore;
int expand;
int contextAlignLength;
bool useLookupTable;
int numBranches;
UInt maxAnchorsPerPosition;
int advanceExactMatches;
int maxLCPLength;
bool stopMappingOnceUnique;
int verbosity;
bool removeEncompassedMatches;
std::ostream *lcpBoundsOutPtr;
int branchExpand;
AnchorParameters();
AnchorParameters &Assign(const AnchorParameters &rhs);
AnchorParameters &operator=(const AnchorParameters &rhs);
};
#endif // _BLASR_ANCHOR_PARAMETERS_HPP_
|
