OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
- ValidParameters validParameter;
+ ValidParameters validParameter("summary.seqs");
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
int tag = 2001;
int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
- vector<long> MPIPos;
+ vector<unsigned long int> MPIPos;
MPI_Status status;
MPI_Status statusOut;
if(processors == 1){
ifstream inFASTA;
openInputFile(fastafile, inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
- inFASTA.close();
- cout << numSeqs << endl;
+ getNumSeqs(inFASTA, numSeqs);
+ inFASTA.close();
+
lines.push_back(new linePair(0, numSeqs));
driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
#else
ifstream inFASTA;
openInputFile(fastafile, inFASTA);
- numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
+ getNumSeqs(inFASTA, numSeqs);
inFASTA.close();
lines.push_back(new linePair(0, numSeqs));
}
#ifdef USE_MPI
/**************************************************************************************/
-int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<long>& MPIPos) {
+int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
try {
int pid;
int SeqSummaryCommand::setLines(string filename) {
try {
- vector<long int> positions;
+ vector<unsigned long int> positions;
ifstream inFASTA;
openInputFile(filename, inFASTA);
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 numFastaSeqs = positions.size();
FILE * pFile;
- long size;
+ unsigned long int size;
//get num bytes in file
pFile = fopen (filename.c_str(),"rb");
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;
}else{
- long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
+ unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
}
lines.push_back(new linePair(startPos, numSeqsPerProcessor));
}