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#include <fstream>
#include <iostream>
#include <string>
#include <random>
#include <seqan/arg_parse.h>
#include <seqan/store.h>
#include <seqan/parallel.h>
#ifdef _OPENMP
#include <omp.h>
#endif
using namespace seqan2;
template <typename TReads, typename TErrorDist, typename TStore>
void simulateReads(TReads & reads, TErrorDist const & errorDist, TStore const & store)
{
String<std::mt19937 > rng;
#ifdef _OPENMP
resize(rng, omp_get_max_threads());
#else
resize(rng, 1);
#endif
std::uniform_int_distribution<unsigned> distContig(0, length(store.contigStore) - 1);
std::uniform_int_distribution<unsigned> distOrientation(0, 1);
std::uniform_real_distribution<double> distFrac(0.0, 1.0);
std::uniform_int_distribution<unsigned> distSubstitute(1, 3);
unsigned readLen = length(errorDist);
SEQAN_OMP_PRAGMA(parallel for)
for (int i = 0; i < (int)length(reads); ++i)
{
unsigned id = 0;
#ifdef _OPENMP
id = omp_get_thread_num();
#endif
unsigned contigId = distContig(rng[id]);
unsigned pos;
bool ok;
do
{
std::uniform_int_distribution<unsigned> distPos(0, length(store.contigStore[contigId].seq) - readLen);
pos = distPos(rng[id]);
reads[i] = infix(store.contigStore[contigId].seq, pos, pos + readLen);
ok = true;
for (unsigned j = 0; j < readLen; ++j)
if (ordValue(reads[i][j]) == 4)
{
ok = false;
break;
}
}
while (!ok);
if (distOrientation(rng[id]) == 1)
reverseComplement(reads[i]);
for (unsigned j = 0; j < readLen; ++j)
{
if (distFrac(rng[id]) < errorDist[j])
{
reads[i][j] = (Dna5)((ordValue(reads[i][j]) + distSubstitute(rng[id])) & 3);
assignQualityValue(reads[i][j], 0);
}
else
assignQualityValue(reads[i][j], 40);
}
}
}
int main(int argc, const char * argv[])
{
//////////////////////////////////////////////////////////////////////////////
// Define options
ArgumentParser parser;
addUsageLine(parser, "[OPTION]... <reference.fasta> <error_dist file>");
CharString outputFilename = "reads.fa";
unsigned numReads = 1000000;
String<double> errorProb;
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "REFERENCE FILE"));
addArgument(parser, ArgParseArgument(ArgParseArgument::INPUT_FILE, "ERROR DIST FILE"));
addOption(parser, ArgParseOption("n", "num-reads", "number of reads", ArgParseOption::INTEGER));
addOption(parser, ArgParseOption("o", "output", "output read filename", ArgParseOption::STRING));
ArgumentParser::ParseResult res = parse(parser, argc, argv);
if (res != ArgumentParser::PARSE_OK)
return res == ArgumentParser::PARSE_ERROR;
//////////////////////////////////////////////////////////////////////////////
// Extract and check options
getOptionValue(numReads, parser, "num-reads");
getOptionValue(outputFilename, parser, "output");
CharString distFile;
getArgumentValue(distFile, parser, 1);
std::ifstream errorDistFile(toCString(distFile), std::ios_base::in | std::ios_base::binary);
while (true)
{
double error;
errorDistFile >> error;
if (!errorDistFile.good())
break;
appendValue(errorProb, error);
}
FragmentStore<> store;
CharString referenceFile;
getArgumentValue(distFile, parser, 0);
if (!loadContigs(store, toCString(referenceFile)))
{
std::cerr << "Failed to load genome." << std::endl;
return 1;
}
//////////////////////////////////////////////////////////////////////////////
// Simulate reads
String<String<Dna5Q> > reads;
resize(reads, numReads);
simulateReads(reads, errorProb, store);
//////////////////////////////////////////////////////////////////////////////
// Output losses to file
std::ofstream readFile(toCString(outputFilename));
for (unsigned i = 0; i < length(reads); ++i)
{
readFile << "@read" << i << std::endl;
readFile << reads[i] << std::endl;
readFile << "+" << std::endl;
for (unsigned j = 0; j < length(reads[i]); ++j)
readFile << (char)('!' + getQualityValue(reads[i][j]));
readFile << std::endl;
}
return 0;
}
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