OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("align.seqs");
map<string, string>::iterator it;
//check to make sure all parameters are valid for command
int ableToOpen;
ifstream in;
-
- #ifdef USE_MPI
- int pid;
- MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
- MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
-
- if (pid == 0) {
- #endif
- ableToOpen = openInputFile(candidateFileNames[i], in);
- in.close();
-
- #ifdef USE_MPI
- for (int j = 1; j < processors; j++) {
- MPI_Send(&ableToOpen, 1, MPI_INT, j, 2001, MPI_COMM_WORLD);
- }
- }else{
- MPI_Status status;
- MPI_Recv(&ableToOpen, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+ ableToOpen = openInputFile(candidateFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + getSimpleName(candidateFileNames[i]);
+ m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ableToOpen = openInputFile(tryPath, in, "noerror");
+ candidateFileNames[i] = tryPath;
}
-
- #endif
+ }
+ in.close();
if (ableToOpen == 1) {
- m->mothurOut(candidateFileNames[i] + " will be disregarded."); m->mothurOutEndLine();
+ m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
//erase from file list
candidateFileNames.erase(candidateFileNames.begin()+i);
i--;
#ifdef USE_MPI
int pid, end, numSeqsPerProcessor;
int tag = 2001;
- vector<long> MPIPos;
+ vector<unsigned long int> MPIPos;
MPIWroteAccnos = false;
-
+
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
MPI_Comm_size(MPI_COMM_WORLD, &processors);
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
int inMode=MPI_MODE_RDONLY;
- //char* outAlignFilename = new char[alignFileName.length()];
- //memcpy(outAlignFilename, alignFileName.c_str(), alignFileName.length());
-
char outAlignFilename[1024];
strcpy(outAlignFilename, alignFileName.c_str());
-
- //char* outReportFilename = new char[reportFileName.length()];
- //memcpy(outReportFilename, reportFileName.c_str(), reportFileName.length());
char outReportFilename[1024];
strcpy(outReportFilename, reportFileName.c_str());
-
- //char* outAccnosFilename = new char[accnosFileName.length()];
- //memcpy(outAccnosFilename, accnosFileName.c_str(), accnosFileName.length());
char outAccnosFilename[1024];
strcpy(outAccnosFilename, accnosFileName.c_str());
-
- //char* inFileName = new char[candidateFileNames[s].length()];
- //memcpy(inFileName, candidateFileNames[s].c_str(), candidateFileNames[s].length());
char inFileName[1024];
strcpy(inFileName, candidateFileNames[s].c_str());
}
}
else{
- vector<int> positions;
+ vector<unsigned long int> positions;
processIDS.resize(0);
ifstream inFASTA;
while(!inFASTA.eof()){
input = getline(inFASTA);
if (input.length() != 0) {
- if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+ if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
}
}
inFASTA.close();
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
- long int startPos = positions[ i * numSeqsPerProcessor ];
+ unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
if(i == processors - 1){
numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
}
//if there is a possibility that this sequence should be reversed
if (candidateSeq->getNumBases() < numBasesNeeded) {
- string wasBetter = "";
+ string wasBetter = "";
//if the user wants you to try the reverse
if (flip) {
//get reverse compliment
delete nast;
nast = nast2;
needToDeleteCopy = true;
+ wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
}else{
- wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
+ wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
delete nast2;
delete copy;
}
}
//**********************************************************************************************************************
#ifdef USE_MPI
-int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<long>& MPIPos){
+int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long int>& MPIPos){
try {
string outputString = "";
MPI_Status statusReport;
int length = MPIPos[start+i+1] - MPIPos[start+i];
char* buf4 = new char[length];
- memcpy(buf4, outputString.c_str(), length);
+ //memcpy(buf4, outputString.c_str(), length);
MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
delete buf4;
if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length); }
- istringstream iss (tempBuf,istringstream::in);
+ istringstream iss (tempBuf,istringstream::in);
+
Sequence* candidateSeq = new Sequence(iss);
+
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
int numBasesNeeded = origNumBases * threshold;
projects / mothur.git / blobdiff