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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: index.hpp
* created: Nov 06, 2017 Mon
*/
#pragma once
#include <vector>
#include <cstdint>
// forward
struct Runopts;
struct kmer;
struct kmer_origin;
class Refstats;
/**
* 1. Each reference file can be indexed into multiple index parts depending on the file size.
* Each index file name follows a pattern <Name_Part> e.g. index1_0, index1_1 etc.
*/
struct Index {
uint16_t index_num; // currrently loaded index number (DB file) Set in Main thread
uint32_t part; // currently loaded index part
uint32_t number_elements; /* number of positions in (L+1)-mer positions table */
bool is_ready; // flags the index is built and ready
// Index stats
//long _match = 0; /* Smith-Waterman score for a match */
//long _mismatch = 0; /* Smith-Waterman score for a mismatch */
//long _gap_open = 0; /* Smith-Waterman score for gap opening */
//long _gap_extension = 0; /* Smith-Waterman score for gap extension */
std::vector<kmer> lookup_tbl; /**< reference to L/2-mer look up table */
std::vector<kmer_origin> positions_tbl; /**< reference to (L+1)-mer positions table */
/*
* Initilize the index.
* If index files do not exist or are empty - build the index.
*/
Index(Runopts & opts);
//~Index() {}
void load(uint32_t idx_num, uint32_t idx_part, std::vector<std::pair<std::string, std::string>>& indexfiles, Refstats & refstats);
void unload();
}; // ~struct Index
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