openInputFile(fastaFile, inFASTA);
getNumSeqs(inFASTA, numSeqs);
inFASTA.close();
- qFile.close();
+
lines.push_back(new linePair(0, numSeqs));
driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[0]);
+ for (int j = 0; j < fastaFileNames.size(); j++) {
+ rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
+ }
+ if(qFileName != ""){
+ for (int j = 0; j < qualFileNames.size(); j++) {
+ rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
+ }
+ }
+
if (m->control_pressed) { return 0; }
#endif
Sequence currSeq(inFASTA);
QualityScores currQual;
if(qFileName != ""){
- currQual = QualityScores(qFile);
+ currQual = QualityScores(qFile, currSeq.getNumBases());
}
string origSeq = currSeq.getUnaligned();