MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI); //comm, filename, mode, info, filepointer
if (pid == 0) {
- positions = setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
+ positions = m->setFilePosFasta(fastaFileName, numSeqs); //fills MPIPos, returns numSeqs
//send file positions to all processes
for(int i = 1; i < processors; i++) {
if (temp.getName() != "") {
templateSequences.push_back(temp);
//save longest base
- if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
+ if (temp.getUnaligned().length() >= longest) { longest = temp.getUnaligned().length()+1; }
}
}
#else
ifstream fastaFile;
- openInputFile(fastaFileName, fastaFile);
+ m->openInputFile(fastaFileName, fastaFile);
while (!fastaFile.eof()) {
- Sequence temp(fastaFile); gobble(fastaFile);
+ Sequence temp(fastaFile); m->gobble(fastaFile);
if (m->control_pressed) { templateSequences.clear(); break; }
if (temp.getName() != "") {
templateSequences.push_back(temp);
//save longest base
- if (temp.getUnaligned().length() > longest) { longest = temp.getUnaligned().length()+1; }
+ if (temp.getUnaligned().length() >= longest) { longest = (temp.getUnaligned().length()+1); }
}
}
fastaFile.close();
-
#endif
numSeqs = templateSequences.size();
ifstream kmerFileTest(kmerDBName.c_str());
if(kmerFileTest){
- bool GoodFile = checkReleaseVersion(kmerFileTest, m->getVersion());
+ bool GoodFile = m->checkReleaseVersion(kmerFileTest, m->getVersion());
if (GoodFile) { needToGenerate = false; }
}
#endif