-
Notifications
You must be signed in to change notification settings - Fork 68
/
otumap.h
64 lines (55 loc) · 2.24 KB
/
otumap.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
/*
@copyright 2016-2021 Clarity Genomics BVBA
@copyright 2012-2016 Bonsai Bioinformatics Research Group
@copyright 2014-2016 Knight Lab, Department of Pediatrics, UCSD, La Jolla
@parblock
SortMeRNA - next-generation reads filter for metatranscriptomic or total RNA
This is a free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
SortMeRNA 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 Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License
along with SortMeRNA. If not, see <http://www.gnu.org/licenses/>.
@endparblock
@contributors Jenya Kopylova jenya.kopylov@gmail.com
Laurent Noé laurent.noe@lifl.fr
Pierre Pericard pierre.pericard@lifl.fr
Daniel McDonald wasade@gmail.com
Mikaël Salson mikael.salson@lifl.fr
Hélène Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
#pragma once
#include <string>
#include <vector>
#include <map>
// forward
struct Runopts;
class Refstats;
struct Readstats;
class Readfeed;
class References;
class KeyValueDatabase;
class OtuMap {
// Clustering of reads around references by similarity i.e. {ref: [read, read, ...] , ref : [read, read...] , ...}
// calculated after alignment is done on all reads
// TODO: Store in DB ? Can be very big.
std::vector<std::map<std::string, std::vector<std::string>>> mapv;
//std::map<std::string, std::vector<std::string>> otu_map;
// |_Ref_ID |_Read_IDs
public:
std::filesystem::path fmap;
uint64_t total_otu; // total count of OTU groups in otu_map
public:
OtuMap(int numThreads=1);
void push(int idx, std::string& ref_seq_str, std::string& read_seq_str);
void merge();
void write();
void init(Runopts& opts);
size_t count_otu();
};
void fill_otu_map(Readfeed& readfeed, Readstats& readstats, KeyValueDatabase& kvdb, Runopts& opts, bool is_write=true);