CRef<CSeq_entry> CShortReadFastaInputSource::x_ReadFastqOneSeq(CRef<ILineReader> line_reader) { CTempString line; CTempString id; CRef<CSeq_entry> retval; // first read defline ++(*line_reader); line = **line_reader; // skip empty lines while (!line_reader->AtEOF() && line.empty()) { ++(*line_reader); line = **line_reader; } if (line[0] != '@') { NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:" " defline expected at line: " + NStr::IntToString(line_reader->GetLineNumber())); } id = x_ParseDefline(line); CRef<CSeq_id> seqid(new CSeq_id); seqid->Set(CSeq_id::e_Local, id); // read sequence ++(*line_reader); line = **line_reader; // skip empty lines while (!line_reader->AtEOF() && line.empty()) { ++(*line_reader); line = **line_reader; } // set up sequence if (line.length() > 0) { CRef<CSeq_entry> seq_entry(new CSeq_entry); CBioseq& bioseq = seq_entry->SetSeq(); bioseq.SetInst().SetMol(CSeq_inst::eMol_na); bioseq.SetInst().SetRepr(CSeq_inst::eRepr_raw); bioseq.SetId().clear(); bioseq.SetId().push_back(seqid); bioseq.SetInst().SetLength(line.length()); bioseq.SetInst().SetSeq_data().SetIupacna(CIUPACna(line.data())); bioseq.SetDescr(); m_BasesAdded += line.length(); retval = seq_entry; } // read and skip second defline ++(*line_reader); line = **line_reader; // skip empty lines while (!line_reader->AtEOF() && line.empty()) { ++(*line_reader); line = **line_reader; } if (line[0] != '+') { NCBI_THROW(CInputException, eInvalidInput, (string)"FASTQ parse error:" " defline expected at line: " + NStr::IntToString(line_reader->GetLineNumber())); } // read and skip quality scores ++(*line_reader); line = **line_reader; // skip empty lines while (!line_reader->AtEOF() && line.empty()) { ++(*line_reader); line = **line_reader; } return retval; }