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));
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));
}