- templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0);
+ templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand());
- char buf[length];
- strcpy(buf, outString.c_str());
+ char* buf = new char[length];
+ memcpy(buf, outString.c_str(), length);
MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
MPI_File_write_shared(out, buf, length, MPI_CHAR, &status);
if (svg) {
if (name != "") { //if user has specific names
map<string, string>::iterator it = names.find(querySeq->getName());
if (svg) {
if (name != "") { //if user has specific names
map<string, string>::iterator it = names.find(querySeq->getName());
strcpy(inFileName, namefile.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
MPI_File_get_size(inMPI, &size);
strcpy(inFileName, namefile.c_str());
MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
MPI_File_get_size(inMPI, &size);
MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
string tempBuf = buffer;
if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
istringstream iss (tempBuf,istringstream::in);
MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
string tempBuf = buffer;
if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size); }
istringstream iss (tempBuf,istringstream::in);
- for (small = query.begin(); small != query.end(); small++) {
- large = subject.find(small->first);
+ for (smallone = query.begin(); smallone != query.end(); smallone++) {
+ largeone = subject.find(smallone->first);
- for (small = subject.begin(); small != subject.end(); small++) {
- large = query.find(small->first);
+ for (smallone = subject.begin(); smallone != subject.end(); smallone++) {
+ largeone = query.find(smallone->first);
MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outSVG); //comm, filename, mode, info, filepointer
MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outSVG); //comm, filename, mode, info, filepointer
- char buf2[length];
- strcpy(buf2, outString.c_str());
+ char* buf2 = new char[length];
+ memcpy(buf2, outString.c_str(), length);
MPI_File_write(outSVG, buf2, length, MPI_CHAR, &status);
MPI_File_write(outSVG, buf2, length, MPI_CHAR, &status);