Commit da748db6 authored by Carsten Kemena's avatar Carsten Kemena

[bugfix] clear filestate to enable seekg, disabled threading

parent 23cdd395
Subproject commit 9e07b28bc1fa57600877d964f7aea8bc740aedac
Subproject commit 07584c24f36a0272d98f071b6ff8f018e988d0be
......@@ -112,6 +112,7 @@ DBAccess::search(BSDL::AlignmentMatrix<int, BSDL::DSM> &matrix, bool all, bool c
for (auto &pos : positions)
{
// get the domain arrangement at the given position
this->arrangementDB_.clear();
this->arrangementDB_.seekg(pos, std::ios_base::beg);
getline(this->arrangementDB_, line);
auto domains = BSDL::split(line, ">;");
......
......@@ -116,14 +116,14 @@ main(int argc, char *argv[])
fs::path prefix;
vector<std::string> q, domains;
unsigned short nThreads;
unsigned short nThreads = 1;
po::options_description general("General options");
general.add_options()
("help,h", "Produces this help message")
("db,d", po::value<fs::path>(&prefix)->required()->value_name("FILE"), "The database prefix")
("out,o", po::value<fs::path>(&outFile)->value_name("FILE"), "The output file")
("list-alignments,l", po::value<bool>(&listAlignments)->default_value(false)->zero_tokens(), "List alignments")
("threads,n", po::value<unsigned short>(&nThreads)->default_value(1)->value_name("INT"), "The number of threads to use")
//("threads,n", po::value<unsigned short>(&nThreads)->default_value(1)->value_name("INT"), "The number of threads to use")
;
po::options_description queryOpts("Query options");
......@@ -275,7 +275,7 @@ main(int argc, char *argv[])
size_t nDAs = querySet.size();
#pragma omp parallel for shared(outS, matrices, db, all, minScore, querySet, nDAs)
#pragma omp parallel for shared(outS, matrices, all, minScore, querySet, nDAs, db)
for (size_t i=0; i<nDAs; ++i)
{
auto it=querySet.begin();
......
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