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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: alignment.hpp
* @brief Function and variable definitions for alignment.cpp
*/
#pragma once
#include <map>
#include <queue>
#include <algorithm>
#include "traverse_bursttrie.hpp"
#include "ssw.hpp"
// forward
class Read;
struct Runopts;
struct Index;
class References;
class Output;
struct Readstats;
class Refstats;
using namespace std;
/*! @brief Number of slots by which to dynamically
increment the array storing all alignments
per read */
#define BEST_HITS_INCREMENT 100
/*! @brief Euler's constant */
#define EXP 2.71828182845904523536
/*! @brief Type mypair
A data structure holding two variables
of type uint32_t.
*/
typedef pair<uint32_t,uint32_t> uint32pair;
/*! @fn smallest()
@brief Determine the smallest integer.
@details The mypair data structure holds two integers,
the first being the position a k-mer occurs
on the reference sequence and the second
being the position a k-mer occurs on the
query sequence. This function takes two
mypair data structures and returns the
@param const pair<uint32_t,uint32_t> &a
@param const pair<uint32_t,uint32_t> &b
@return smallest integer of a and b, or a if a == b
*/
//inline bool smallest ( const uint32pair &a, const uint32pair &b );
/*! @fn largest()
@brief Return the largest integer of two input integers
@param const mypair &a
@param const mypair &b
@return 'a' goes before 'b' if a.first > b.first, otherwise
'a'
*/
//bool largest ( const uint32pair &a, const uint32pair &b );
/*! @fn find_lis()
* @brief Given a list of matching positions on the read, find the longest
strictly increasing subsequence, O(n log k)
@param deque<pair<uint32_t, uint32_t> > &a list of matching positions on the read which fall within a range of the read's length on the genome
@param vector<uint32_t> &b array of starting positions of each longest subsequence
*/
void find_lis(deque<pair<uint32_t, uint32_t> > &a, vector<uint32_t> &b);
/*! @brief struct alignment_struct
holds the index of the minimum and maximum scoring
alignments in an array of alignments pointed to by
s_align* ptr */
struct alignment_struct
{
uint32_t max_size; // max size of s_align array
uint32_t size; // actual size of s_align array
uint32_t min_index;
uint32_t max_index;
s_align* ptr;
alignment_struct(): max_size(0), size(0), min_index(0), max_index(0), ptr(0) {}
alignment_struct(uint32_t max_size,
uint32_t size,
uint32_t min,
uint32_t max,
s_align* p) : max_size(max_size), size(size), min_index(min), max_index(max), ptr(p) {}
};
/*
* called on each idx * part * read * strand * [1..max opts.skiplengths[index_num].size (3 by default)]
*
* @param read
* @param opts
* @param index
* @param refs
* @param readstats
* @param refstats
* @param search OUT
* return 'True' to indicate keep searching for more seed matches and better alignment.
* return 'False' - stop search, the alignment is found
* @param max_SW_score the maximum SW score attainable for this read i.e. perfect match
*/
void compute_lis_alignment(Read& read, Runopts& opts, Index& index, References& refs,
Readstats& readstats, Refstats& refstats, bool& search, uint32_t max_SW_score);
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