432 	const FastaRecord &read1,  in merge()
433 	const FastaRecord &read2,  in merge()
450 	vector<FastaRecord>& paths = result.mergedSeqs;  in merge()
533 	FastaRecord &record,  in insertIntoScaffold()
567 std::pair<FastaRecord, FastaRecord>
568 makePseudoReads(std::string seq, FastaRecord record, const Gap& gap)  in makePseudoReads()
570 	std::pair<FastaRecord, FastaRecord> scaftigs;  in makePseudoReads()
591 	map<FastaRecord, map<FastaRecord, Gap> > &flanks,  in kRun()  argument
597 	map<FastaRecord, map<FastaRecord, Gap> >::iterator read1_it;  in kRun()
598 	map<FastaRecord, Gap>::iterator read2_it;  in kRun()
621 	vector<map<FastaRecord, map<FastaRecord, Gap> >::iterator> flanks_closed;  in kRun()
624 		FastaRecord read1 = read1_it->first;  in kRun()
631 			FastaRecord read2 = read2_it->first;  in kRun()
660 …for (vector<map<FastaRecord, map<FastaRecord, Gap> >::iterator>::iterator it = flanks_closed.begin…  in kRun()
697 bool operator<(const FastaRecord& a, const FastaRecord& b)  in operator <()
705 void findFlanks(FastaRecord &record,  in findFlanks()
708 	map<FastaRecord, map<FastaRecord, Gap> > &flanks)  in findFlanks()  argument
735 		std::pair<FastaRecord, FastaRecord> scaftigs =  in findFlanks()
966 	map<FastaRecord, map<FastaRecord, Gap> > flanks;  in main()
973 	for (FastaRecord record;;) {  in main()
991 		map<FastaRecord, map<FastaRecord, Gap> >::iterator read1_it;  in main()
992 		map<FastaRecord, Gap>::iterator read2_it;  in main()
1005 			FastaRecord read1 = read1_it->first;  in main()
1007 				FastaRecord read2 = read2_it->first;  in main()
1096 	for (FastaRecord record;;) {  in main()