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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: readstats.hpp
* created: Nov 06, 2017 Mon
*
* Collective Statistics for all Reads. Encapsulates old 'compute_read_stats' logic and results
* Some statistics computed during Alignment, and some in Post-processing
*/
#pragma once
#include <cstdint>
#include <string>
#include <vector>
#include <map>
#include <mutex>
#include <atomic>
#include "common.hpp"
#include "options.hpp"
// forward
class KeyValueDatabase;
/*
* 1. 'all_reads_count' - Should be known before processing and index loading.
* 2. 'total_mapped_sw_id_cov'
* Calculated during alignment and stored to KVDB
* Thread accessed - Synchronize
* 3. 'reads_matched_per_db' - Synchronize.
* Calculated during alignment. Thread accessed.
* 4. 'total_reads_denovo_clustering'
* TODO: currently accessed in single thread ('computeStats') but potentially could be multiple threads
*/
struct Readstats
{
std::string dbkey; // Hashed concatenation of underscore separated basenames of the read files. Used as the key into the Key-value DB.
std::string suffix; // 'fasta' | 'fastq' TODO: remove?
uint64_t all_reads_count; // [1] total number of reads in file.
uint64_t all_reads_len; // total number of nucleotides in all reads i.e. sum of length of All read sequences
uint32_t min_read_len; // shortest Read length. (read only)
uint32_t max_read_len; // longest Read length. (read only)
uint64_t total_otu; // not to store in DB
std::atomic<uint64_t> num_aligned; // reads passing E-value threshold.
std::atomic<uint64_t> n_yid_ncov; // SW + ID - COV i.e. aligned passing ID, failing COV
std::atomic<uint64_t> n_nid_ycov; // SW - ID + COV i.e. aligned failing ID, passing COV
std::atomic<uint64_t> n_yid_ycov; // [2] SW + ID + COV i.e. aligned passing ID, passing COV
std::atomic<uint64_t> num_denovo; // [4] SW - ID - COV i.e. 'de novo' reads, aligned failing ID, failing COV
std::atomic<uint64_t> num_short; // count of reads shorter than a threshold of N nucleotides. Reset for each index.
std::vector<uint64_t> reads_matched_per_db; // [3] reads matched per database.
// |_TODO: should be atomic std::atomic<uint64_t> 20201019
bool is_stats_calc; // flags 'computeStats' was called.
bool is_set_aligned_id_cov; // flag 'total_aligned_id_cov' was calculated (so no need to calculate no more)
Readstats(uint64_t all_reads_count, uint64_t all_reads_len, uint32_t min_read_len, uint32_t max_read_len, KeyValueDatabase& kvdb, Runopts& opts);
void calcSuffix(Runopts& opts);
std::string toBstring();
std::string toString();
bool restoreFromDb(KeyValueDatabase & kvdb);
void store_to_db(KeyValueDatabase & kvdb);
void set_is_set_aligned_id_cov();
}; // ~struct Readstats
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