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// Author Martin C. Frith 2023
// SPDX-License-Identifier: GPL-3.0-or-later
// This struct records coverage of "diagonals" by gapless alignments,
// when comparing two sequences. The diagonal is the coordinate in
// one sequence minus the coordinate in the other sequence. We assume
// that one sequence is scanned sequentially, and the other is
// accessed randomly. We record the furthest sequential position
// covered so far in each diagonal. This lets us avoid triggering
// gapless alignments in places that are already covered.
// Since the number of diagonals may be huge, we map them to a smaller
// number of bins. To keep the bin populations small, when checking
// if a position is covered, we discard information about earlier
// sequential positions.
#ifndef DIAGONALTABLE_HH
#define DIAGONALTABLE_HH
#include <stddef.h>
#include <utility> // pair
#include <vector>
namespace cbrc {
struct DiagonalTable {
typedef std::pair<size_t, size_t> pairT;
enum { BINS = 256 }; // use a power-of-two for faster modulus (maybe)
// 256 is much faster than 65536 in my tests
// is this position on this diagonal already covered by an alignment?
bool isCovered(size_t diagonal, size_t sequentialPos) {
std::vector<pairT> &v = hits[diagonal % BINS];
for (std::vector<pairT>::iterator i = v.begin(); i < v.end(); ) {
if (i->first >= sequentialPos) {
if (i->second == diagonal) return true;
++i;
} else {
i = v.erase(i); // hopefully we rarely get here
}
}
return false;
}
// add an alignment endpoint to the table:
void addEndpoint(size_t diagonal, size_t sequentialPos) {
hits[diagonal % BINS].push_back(pairT(sequentialPos, diagonal));
}
std::vector<pairT> hits[BINS];
};
}
#endif
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