int start = time(NULL);
#ifdef USE_MPI
- int pid, end, numSeqsPerProcessor;
+ int pid, numSeqsPerProcessor;
int tag = 2001;
vector<unsigned long int> MPIPos;
MPIWroteAccnos = false;
if (m->control_pressed) { return 0; }
Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
-
+ report.setCandidate(candidateSeq);
+
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
int numBasesNeeded = origNumBases * threshold;
accnosFile << candidateSeq->getName() << wasBetter << endl;
}
- report.setCandidate(candidateSeq);
report.setTemplate(templateSeq);
report.setSearchParameters(search, searchScore);
report.setAlignmentParameters(align, alignment);
istringstream iss (tempBuf,istringstream::in);
Sequence* candidateSeq = new Sequence(iss);
-
+ report.setCandidate(candidateSeq);
+
int origNumBases = candidateSeq->getNumBases();
string originalUnaligned = candidateSeq->getUnaligned();
int numBasesNeeded = origNumBases * threshold;
MPIWroteAccnos = true;
}
- report.setCandidate(candidateSeq);
report.setTemplate(templateSeq);
report.setSearchParameters(search, searchScore);
report.setAlignmentParameters(align, alignment);