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/*
@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 No laurent.noe@lifl.fr
Pierre Pericard pierre.pericard@lifl.fr
Daniel McDonald wasade@gmail.com
Mikal Salson mikael.salson@lifl.fr
Hlne Touzet helene.touzet@lifl.fr
Rob Knight robknight@ucsd.edu
*/
/*
* FILE: references.hpp
* Created: Nov 06, 2017 Mon
*/
#pragma once
#include <cstdint>
#include <string>
#include <vector>
#include <algorithm>
#include "common.hpp" // Format, FASTA_HEADER_START, FASTQ_HEADER_START
// forward
class Refstats;
struct Runopts;
class References {
public:
struct BaseRecord
{
size_t nid; // position of the sequence in the Reference file [0...'number of sequences in the ref.file - 1']
std::string id; // ID from header
std::string header;
std::string sequence;
std::string quality; // "" (fasta) | "xxx..." (fastq)
BIO_FORMAT format; // FASTA | FATSQ
bool isEmpty;
BaseRecord(): isEmpty(true) {}
void clear()
{
header.clear();
sequence.clear();
quality.clear();
isEmpty = true;
}
std::string getId() {
std::string id = header.substr(0, header.find(' '));
id.erase(id.begin(), std::find_if(id.begin(), id.end(), [](auto ch) {return !(ch == FASTA_HEADER_START || ch == FASTQ_HEADER_START);}));
return id;
}
};
std::vector<BaseRecord> buffer; // Container for references TODO: change name?
References(): num(0), part(0) {}
//~References() {}
void load(uint32_t idx_num, uint32_t idx_part, Runopts & opts, Refstats & refstats); // load references into the buffer given index number and index part
void convert_fix(std::string & seq); // convert sequence to numberical form and fix ambiguous chars
std::string convertChar(int idx); // convert numerical form to char string
/*
* For debugging needs.
* find a reference index given a header.
*/
int findref(const std::string& id);
void unload();
public:
uint16_t num; // number of the reference file currently loaded
uint16_t part; // part of the reference file currently loaded
//private:
// bool load_for_search;
}; // ~class References
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