291 	unsigned readNo = -1;  in countCoocurrences()  local
298 		if ((*it).rseqNo == readNo)  in countCoocurrences()
308 			readNo = (*it).rseqNo;  in countCoocurrences()
497 	unsigned readNo = -1;  in assignMappingQuality()  local
512 		readNo = (*it).rseqNo;  in assignMappingQuality()
515 		if(++it!=itEnd && (*it).rseqNo==readNo)  in assignMappingQuality()
520 			secondBestMatches = cnts[1][readNo] >> 5;  in assignMappingQuality()
551 					int q = getQualityValue(reads[readNo][j]);//(int)((unsigned char)(reads[readNo][j])>>3);  in assignMappingQuality()
639 	unsigned readNo = 0;  in dumpUnmappedReads()  local
641 	while(mIt != mEnd && readNo < length(reads))  in dumpUnmappedReads()
643 		while((*mIt).rseqNo > readNo)  in dumpUnmappedReads()
646 			file << headerChar << readIDs[readNo] << std::endl << reads[readNo] << std::endl;  in dumpUnmappedReads()
650 				for(unsigned j=0;j<length(reads[readNo]);++j)  in dumpUnmappedReads()
651 					file << (char)(getQualityValue(reads[readNo][j])+ 33);  in dumpUnmappedReads()
654 			++readNo;  in dumpUnmappedReads()
656 		while((*mIt).rseqNo == readNo && mIt != mEnd)  in dumpUnmappedReads()
660 		++readNo;  in dumpUnmappedReads()
664 	while(readNo < length(reads))  in dumpUnmappedReads()
667 		file << headerChar << readIDs[readNo] << std::endl << reads[readNo] << std::endl;  in dumpUnmappedReads()
671 			for(unsigned j=0;j<length(reads[readNo]);++j)  in dumpUnmappedReads()
672 				file << (char)(getQualityValue(reads[readNo][j])+ 33);  in dumpUnmappedReads()
675 		++readNo;  in dumpUnmappedReads()
1038 			for(unsigned readNo = 0; readNo < length(reads); ++readNo)  in dumpMatches()  local
1044 						file << '>' << readIDs[readNo] << _sep_;  in dumpMatches()
1050 						file << readName << '#' << ::std::setw(pzeros) << readNo + 1  << _sep_;  in dumpMatches()
1054 				if (it == itEnd || readNo < (*it).rseqNo)  in dumpMatches()
1056 					if (!empty(reads[readNo]))  in dumpMatches()
1057 …file << reads[readNo] << _sep_ << "NM" << _sep_ << '0' << _sep_ << '0' << _sep_ << '0' << ::std::e…  in dumpMatches()
1066 					file << reads[readNo] << _sep_;  in dumpMatches()
1069 						bestMatches = stats[(*it).editDist][readNo];  in dumpMatches()
1075 …file << (*it).editDist << _sep_ << stats[0][readNo] << _sep_ << stats[1][readNo] << _sep_ << stats…  in dumpMatches()
1104 								if ((options.compMask[ordValue(reads[readNo][i])] &   in dumpMatches()