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#ifndef RRESOLVER_RALGORITHMS_SHORT_H
#define RRESOLVER_RALGORITHMS_SHORT_H 1
#include "RUtils.h"
#include "BloomFilters.h"
#include "Contigs.h"
#include "SequenceTree.h"
#include "Common/Histogram.h"
#include <vector>
#include <string>
#include <cassert>
#include <fstream>
#include <climits>
#include <cmath>
const int MIN_MARGIN = 2;
const int MAX_TESTS_OFFSET = 16;
const int R_VALUES_STEP = 20;
const int R_STEPS_MAX = 1;
const int R_MAX_K_DIFF = 80;
const int MAX_SUBITERATIONS = 2;
const long HIST_SAMPLE_SIZE = LONG_MAX;
const long REPEAT_CASES_LIMIT = LONG_MAX;
const int RMER_QUALITY_THRESHOLD = 30;
const long READ_STATS_SAMPLE_SIZE = 100000;
const double READ_BATCH_FRACTION_THRESHOLD = 0.30;
const long PATH_COMBINATIONS_MULTITHREAD_THRESHOLD = 5000;
const double SUPPORTED_PATHS_MIN = 0.15;
const double COV_APPROX_FORMULA_FACTOR = 5.00;
const double SPACED_SEEDS_SNP_FRACTION = 1.00;
const int MAX_READ_SIZE = 300;
namespace opt {
/** Read Bloom filter size in bytes. */
extern size_t bloomSize;
/** The number of parallel threads */
extern int threads;
/** Prefix for the histogram files */
extern std::string histPrefix;
/** Name of the file to write resulting graph to */
extern std::string outputGraphPath;
/** Name of the file to write resulting graph to */
extern std::string outputContigsPath;
/** Number of kmers required to be found for a path to be supported */
extern int threshold;
/** Minimum number of sliding window moves */
extern int min_tests;
/** Maximum number of branching paths */
extern int branching;
/** Flag indicating whether error correction is enabled */
extern int error_correction;
/** Name of the file to write supported paths to */
extern std::string outputSupportedPathsPath;
/** Name of the file to write unsupported paths to */
extern std::string outputUnsupportedPathsPath;
extern unsigned k; // used by ContigProperties
extern int format; // used by ContigProperties
}
class Support {
public:
Support() = default;
Support(int calculatedTests): found(-1), tests(-1), calculatedTests(calculatedTests) {
assert(calculatedTests >= 0);
}
Support(int found, int tests):
found(found), tests(tests)
{
assert(found >= 0);
assert(tests > 0);
assert(calculatedTests == -1);
}
Support(int found, int tests, int calculatedTests):
found(found), tests(tests), calculatedTests(calculatedTests)
{
assert(found >= 0);
assert(tests > 0);
assert(calculatedTests >= 0);
}
bool unknown() const {
return tests == -1;
}
void reset() {
found = -1;
tests = -1;
}
bool good() const {
return unknown() || found >= opt::threshold;
}
bool operator>(const Support& s) {
return found > s.found;
}
bool operator<(const Support& s) {
return found < s.found;
}
int found = -1;
int tests = -1;
int calculatedTests = -1;
};
class ReadBatch {
public:
ReadBatch(int size): size(size) {}
double getFractionOfTotal() const { return double(sampleCount) / double(readsSampleSize); }
int size;
std::vector<int> rValues;
Histogram qualThresholdPositions;
long sampleCount = 0;
static long readsSampleSize;
static std::vector<ReadBatch> batches;
static ReadBatch current;
};
void
resolveShort(const std::vector<std::string>& readFilepaths,
ImaginaryContigPaths& supportedPaths,
ImaginaryContigPaths& unsupportedPaths);
#endif
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