public void write(Text key, SequencedFragment seq) throws IOException { // write the id line out.write('@'); if (key != null) out.write(key.getBytes(), 0, key.getLength()); else out.write(makeId(seq).getBytes(UTF8)); out.write('\n'); // write the sequence and separator out.write(seq.getSequence().getBytes(), 0, seq.getSequence().getLength()); out.write(PLUS_LINE); // now the quality if (baseQualityFormat == BaseQualityEncoding.Sanger) out.write(seq.getQuality().getBytes(), 0, seq.getQuality().getLength()); else if (baseQualityFormat == BaseQualityEncoding.Illumina) { buffer.set(seq.getQuality()); SequencedFragment.convertQuality(buffer, BaseQualityEncoding.Sanger, baseQualityFormat); out.write(buffer.getBytes(), 0, buffer.getLength()); } else throw new RuntimeException("FastqOutputFormat: unknown base quality format " + baseQualityFormat); // and the final newline out.write('\n'); }
public void write(Text key, SequencedFragment seq) throws IOException { // write the id line out.write('@'); if (key != null) out.write(key.getBytes(), 0, key.getLength()); else out.write(makeId(seq).getBytes(UTF8)); out.write('\n'); // write the sequence and separator out.write(seq.getSequence().getBytes(), 0, seq.getSequence().getLength()); out.write(PLUS_LINE); // now the quality if (baseQualityFormat == BaseQualityEncoding.Sanger) out.write(seq.getQuality().getBytes(), 0, seq.getQuality().getLength()); else if (baseQualityFormat == BaseQualityEncoding.Illumina) { buffer.set(seq.getQuality()); SequencedFragment.convertQuality(buffer, BaseQualityEncoding.Sanger, baseQualityFormat); out.write(buffer.getBytes(), 0, buffer.getLength()); } else throw new RuntimeException("FastqOutputFormat: unknown base quality format " + baseQualityFormat); // and the final newline out.write('\n'); }
public void write(Text key, SequencedFragment seq) throws IOException { // write the id line out.write('@'); if (key != null) out.write(key.getBytes(), 0, key.getLength()); else out.write(makeId(seq).getBytes(UTF8)); out.write('\n'); // write the sequence and separator out.write(seq.getSequence().getBytes(), 0, seq.getSequence().getLength()); out.write(PLUS_LINE); // now the quality if (baseQualityFormat == BaseQualityEncoding.Sanger) out.write(seq.getQuality().getBytes(), 0, seq.getQuality().getLength()); else if (baseQualityFormat == BaseQualityEncoding.Illumina) { buffer.set(seq.getQuality()); SequencedFragment.convertQuality(buffer, BaseQualityEncoding.Sanger, baseQualityFormat); out.write(buffer.getBytes(), 0, buffer.getLength()); } else throw new RuntimeException("FastqOutputFormat: unknown base quality format " + baseQualityFormat); // and the final newline out.write('\n'); }