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#include "config.h"
#include "NetworkSequenceCollection.h"
#include "Assembly/Options.h"
#include "Common/Log.h"
#include "Common/Options.h"
#include "Common/Timer.h"
#include "Common/Uncompress.h"
#include "DataLayer/FastaReader.h"
#include <cerrno>
#include <climits> // for HOST_NAME_MAX
#include <cstdio> // for setvbuf
#include <cstdlib>
#include <cstring> // for strerror
#include <iostream>
#include <mpi.h>
#include <unistd.h> // for gethostname
#include <vector>
#include "DataBase/DB.h"
using namespace std;
static const char* FASTA_SUFFIX = ".fa";
#if PAIRED_DBG
// Define KmerPair::s_length
# include "PairedDBG/KmerPair.cc"
#endif
static void mergeFastaFiles(const string& outputPath, const string& inputPathPrefix, bool generateNewIds = false)
{
cout << "Concatenating fasta files to " << outputPath << endl;
// write merged FASTA file
FastaWriter writer(outputPath.c_str());
uint64_t seqid = 0;
for(int i = 0; i < opt::numProc; i++) {
ostringstream filename;
filename << inputPathPrefix << i << FASTA_SUFFIX;
assert(filename.good());
string str(filename.str());
FastaReader reader(str.c_str(), FastaReader::NO_FOLD_CASE);
for (FastaRecord rec; reader >> rec;) {
if (generateNewIds)
writer.WriteSequence(rec.seq, seqid++, rec.comment);
else
writer.WriteSequence(rec.seq, rec.id, rec.comment);
}
assert(reader.eof());
}
// remove temp FASTA files
bool die = false;
for (int i = 0; i < opt::numProc; i++) {
ostringstream s;
s << inputPathPrefix << i << FASTA_SUFFIX;
string str(s.str());
const char* path = str.c_str();
if (unlink(path) == -1) {
cerr << "error: removing `" << path << "': "
<< strerror(errno) << endl;
die = true;
}
}
if (die)
exit(EXIT_FAILURE);
}
int main(int argc, char** argv)
{
Timer timer("Total");
// Set stdout to be line buffered.
setvbuf(stdout, NULL, _IOLBF, 0);
MPI_Init(&argc,&argv);
MPI_Comm_rank(MPI_COMM_WORLD, &opt::rank);
MPI_Comm_size(MPI_COMM_WORLD, &opt::numProc);
// OMPI-1.6.1 and later reset the SIGCHLD handler so we need to
// reinitialize uncompress.
uncompress_init();
#if PAIRED_DBG
opt::singleKmerSize = -1;
#endif
opt::parse(argc, argv);
if (opt::rank == 0)
cout << "Running on " << opt::numProc << " processors\n";
MPI_Barrier(MPI_COMM_WORLD);
char hostname[HOST_NAME_MAX];
gethostname(hostname, sizeof hostname);
logger(0) << "Running on host " << hostname << endl;
MPI_Barrier(MPI_COMM_WORLD);
#if PAIRED_DBG
Kmer::setLength(opt::singleKmerSize);
KmerPair::setLength(opt::kmerSize);
#else
Kmer::setLength(opt::kmerSize);
#endif
if (opt::rank == 0) {
NetworkSequenceCollection networkSeqs;
networkSeqs.runControl();
} else {
NetworkSequenceCollection networkSeqs;
networkSeqs.run();
}
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
if (opt::rank == 0) {
mergeFastaFiles(opt::contigsPath, "contigs-", true);
if (!opt::snpPath.empty())
mergeFastaFiles(opt::snpPath, "snp-");
cout << "Done." << endl;
DB db;
if (!opt::db.empty()) {
init(db,
opt::getUvalue(),
opt::getVvalue(),
"ABYSS-P",
opt::getCommand(),
opt::getMetaValue()
);
addToDb(db, "SS", opt::ss);
addToDb(db, "K", opt::kmerSize);
addToDb(db, "numProc", opt::numProc);
addToDb(db, NSC::moveFromAaStatMap());
}
}
return 0;
}
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