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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 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
*/
/*
* @file indexdb.hpp
* @brief Function and variable definitions for indexdb.cpp
*/
#pragma once
#include <sys/types.h>
#include "ssw.h"
#include "common.hpp"
#include "options.hpp"
/*! @brief The size of an entry in a burst trie bucket
Each bucket entry is of ENTRYSIZE bytes. The first
4 bytes are to store the seed (ex. 18-mer) and the
last 4 bytes are to store the index for the
positions lookup table.<br/>
The seed is encoded as 2 bits/nt, such that
16 nucleotides can fit into a 4 byte integer.
*/
#define ENTRYSIZE (2*sizeof(uint32_t))
// maximum number of bytes in a bucket prior to bursting, should be <= L1 cache size and a power of 2 for efficiency
#define THRESHOLD 128
/**
* parse each reference file (FASTA), and build the burst tries
* @return void
*/
int build_index(Runopts &opts);
struct NodeElement
{
// a pointer to a bucket or another trie node
union
{
void* bucket;
NodeElement* trie;
} nodetype;
// current size (in bytes) of bucket
unsigned int size;
// flags whether the node leads to a child trie node, is empty or leads to a bucket node;
// 0 :: empty;
// 1 :: trie node;
// 2 :: bucket
char flag;
};
// the reference sequence number and position at which a 19-mer exists on the sequence; these values *must* be positive
struct seq_pos
{
uint32_t pos; // position on the sequence
uint32_t seq; // the sequence number (in the original reference files?)
};
struct kmer_origin
{
seq_pos* arr; // pointer to seq_pos array
uint32_t size; // number of 19-mer occurrences
};
struct kmer
{
NodeElement* trie_F; // pointer to forward mini burst trie
NodeElement* trie_R; // pointer to reverse mini burst trie
uint32_t count; // count of 9-mers
};
// data structure to store information on index parts
// i.e. index can be partitioned for large reference files
struct index_parts_stats {
unsigned long int start_part; // start of a part in the reference file
unsigned long int seq_part_size; // number of bytes of reference sequences to read
uint32_t numseq_part; // the number of sequences in this part
};
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