int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
#endif
- bool abort, realign, trim, trimera, save, hasName, hasCount;
+ bool abort, realign, trim, trimera, save, hasName, hasCount, dups;
string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
float divR;
inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA);
}
- pDataArray->count = pDataArray->end;
-
if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera; return 0; }
if (chimera->getUnaligned()) {
if (pDataArray->start == 0) { chimera->printHeader(out); }
- int count = 0;
+ pDataArray->count = 0;
for(int i = 0; i < pDataArray->end; i++){
if (pDataArray->m->control_pressed) { out.close(); out2.close(); if (pDataArray->trim) { out3.close(); } inFASTA.close(); delete chimera; return 1; }
}
- count++;
+ pDataArray->count++;
}
delete candidateSeq;
//report progress
- if((count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 == 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
}
//report progress
- if((count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(count)); pDataArray->m->mothurOutEndLine(); }
+ if((pDataArray->count) % 100 != 0){ pDataArray->m->mothurOut("Processing sequence: " + toString(pDataArray->count)); pDataArray->m->mothurOutEndLine(); }
pDataArray->numNoParents = chimera->getNumNoParents();
- if (pDataArray->numNoParents == count) { pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
+ if (pDataArray->numNoParents == pDataArray->count) { pDataArray->m->mothurOut("[WARNING]: megablast returned 0 potential parents for all your sequences. This could be due to formatdb.exe not being setup properly, please check formatdb.log for errors.\n"); }
out.close();
out2.close();