forked from voutcn/megahit
-
Notifications
You must be signed in to change notification settings - Fork 0
/
branch_group.h
82 lines (72 loc) · 2.53 KB
/
branch_group.h
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
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
/*
* MEGAHIT
* Copyright (C) 2014 The University of Hong Kong
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef BRANCH_GROUP_H_
#define BRANCH_GROUP_H_
#include <stdint.h>
#include <vector>
#include "succinct_dbg.h"
class BranchGroup
{
public:
typedef std::vector<int64_t> BranchRecord;
BranchGroup(SuccinctDBG *sdbg, int64_t begin_node, int max_branches = 2, int max_length = 0):
sdbg_(sdbg), begin_node_(begin_node), max_branches_(max_branches), max_length_(max_length), status_(kNotMergedOrCorrected) {
branches_.reserve(max_branches_);
multiplicities_.reserve(max_branches_);
if (max_length <= 0) {
max_length_ = sdbg->kmer_k * 2 + 2;
}
}
BranchGroup(const BranchGroup &rhs):
sdbg_(rhs.sdbg_), begin_node_(rhs.begin_node_), end_node_(rhs.end_node_),
max_branches_(rhs.max_branches_), max_length_(rhs.max_length_), branches_(rhs.branches_),
multiplicities_(rhs.multiplicities_), status_(kNotMergedOrCorrected) { }
BranchGroup& operator= (const BranchGroup &rhs) {
sdbg_ = rhs.sdbg_;
begin_node_ = rhs.begin_node_;
end_node_ = rhs.end_node_;
max_branches_ = rhs.max_branches_;
max_length_ = rhs.max_length_;
branches_ = rhs.branches_;
multiplicities_ = rhs.multiplicities_;
status_ = rhs.status_;
return *this;
}
bool Search();
bool RevSearch();
bool RemoveErrorBranches(double cutoff_ratio = 0.5);
bool Merge();
size_t length() {
if (branches_.size() == 0) { return 0; }
return branches_[0].size();
}
private:
SuccinctDBG *sdbg_;
int64_t begin_node_;
int64_t end_node_;
int64_t max_branches_;
int64_t max_length_;
vector<BranchRecord> branches_;
vector<int> multiplicities_;
enum BranchGroupStatus {
kNotMergedOrCorrected,
kErrorRemoved,
kCannotIdentifyError,
} status_;
};
#endif