if (m->control_pressed) { errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
Sequence query(queryFile);
if (m->control_pressed) { errorSummaryFile.close(); errorSeqFile.close(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
Sequence query(queryFile);
int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
int closestRefIndex = chimeraTest.getClosestRefIndex();
int numParentSeqs = chimeraTest.analyzeQuery(query.getName(), query.getAligned());
int closestRefIndex = chimeraTest.getClosestRefIndex();
// int origLength = report.getQueryLength();
int startBase = report.getQueryStart();
int endBase = report.getQueryEnd();
quality = QualityScores(qualFile);
// int origLength = report.getQueryLength();
int startBase = report.getQueryStart();
int endBase = report.getQueryEnd();
quality = QualityScores(qualFile);
quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
quality.updateQScoreErrorMap(qScoreErrorMap, minCompare.sequence, startBase, endBase, minCompare.weight);
quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
quality.updateForwardMap(qualForwardMap, startBase, endBase, minCompare.weight);
quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);
quality.updateReverseMap(qualReverseMap, startBase, endBase, minCompare.weight);