/** * Create an object of the appropriate type to be used as a value. */ public SequencedFragment createValue() { return new SequencedFragment(); }
/** * Create an object of the appropriate type to be used as a value. */ public SequencedFragment createValue() { return new SequencedFragment(); }
/** * Create an object of the appropriate type to be used as a value. */ public SequencedFragment createValue() { return new SequencedFragment(); }
/** * Create an object of the appropriate type to be used as a value. */ public SequencedFragment createValue() { return new SequencedFragment(); }
/** * Create an object of the appropriate type to be used as a value. */ public SequencedFragment createValue() { return new SequencedFragment(); }
/** * Create an object of the appropriate type to be used as a value. */ public SequencedFragment createValue() { return new SequencedFragment(); }
public SequencedFragment createValue() { return new SequencedFragment(); }
@Before public void setup() { frag = new SequencedFragment(); frag2 = new SequencedFragment(); }
@Before public void setup() throws IOException { tempQseq = File.createTempFile("test_qseq_input_format", "qseq"); tempGz = File.createTempFile("test_qseq_input_format", ".gz"); conf = new JobConf(); key = new Text(); fragment = new SequencedFragment(); }
@Before public void setup() throws IOException { tempFastq = File.createTempFile("test_fastq_input_format", "fastq"); tempGz = File.createTempFile("test_fastq_input_format", ".gz"); conf = new JobConf(); key = new Text(); fragment = new SequencedFragment(); }
private static SequencedFragment cloneBySerialization(SequencedFragment original) throws IOException { ByteArrayOutputStream outputBuffer = new ByteArrayOutputStream(); DataOutputStream dataOutput = new DataOutputStream(outputBuffer); original.write(dataOutput); dataOutput.close(); SequencedFragment newFrag = new SequencedFragment(); newFrag.readFields( new DataInputStream( new ByteArrayInputStream(outputBuffer.toByteArray()))); return newFrag; }
@Before public void setup() throws IOException { fragment = new SequencedFragment(); fragment.setInstrument("instrument"); fragment.setRunNumber(1); fragment.setFlowcellId("xyz"); fragment.setLane(2); fragment.setTile(1001); fragment.setXpos(10000); fragment.setYpos(9999); fragment.setRead(1); fragment.setFilterPassed(true); fragment.setIndexSequence("CATCAT"); fragment.setSequence(new Text("AAAAAAAAAA")); fragment.setQuality(new Text("##########")); outputBuffer = new ByteArrayOutputStream(); dataOutput = new DataOutputStream(outputBuffer); writer = new QseqRecordWriter(new Configuration(), dataOutput); }
@Before public void setup() throws IOException { fragment = new SequencedFragment(); fragment.setInstrument("instrument"); fragment.setRunNumber(1); fragment.setFlowcellId("xyz"); fragment.setLane(2); fragment.setTile(1001); fragment.setXpos(10000); fragment.setYpos(9999); fragment.setRead(1); fragment.setFilterPassed(true); fragment.setControlNumber(33); fragment.setIndexSequence("CATCAT"); fragment.setSequence(new Text("AAAAAAAAAA")); fragment.setQuality(new Text("##########")); outputBuffer = new ByteArrayOutputStream(); dataOutput = new DataOutputStream(outputBuffer); writer = new FastqRecordWriter(new Configuration(), dataOutput); }