private boolean scanIlluminaId(Text name, SequencedFragment fragment) { Matcher m = ILLUMINA_PATTERN.matcher(name.toString()); boolean matches = m.matches(); if (matches) { fragment.setInstrument(m.group(1)); fragment.setRunNumber(Integer.parseInt(m.group(2))); fragment.setFlowcellId(m.group(3)); fragment.setLane(Integer.parseInt(m.group(4))); fragment.setTile(Integer.parseInt(m.group(5))); fragment.setXpos(Integer.parseInt(m.group(6))); fragment.setYpos(Integer.parseInt(m.group(7))); fragment.setRead(Integer.parseInt(m.group(8))); fragment.setFilterPassed("N".equals(m.group(9))); fragment.setControlNumber(Integer.parseInt(m.group(10))); fragment.setIndexSequence(m.group(11)); } return matches; }
private boolean scanIlluminaId(Text name, SequencedFragment fragment) { Matcher m = ILLUMINA_PATTERN.matcher(name.toString()); boolean matches = m.matches(); if (matches) { fragment.setInstrument(m.group(1)); fragment.setRunNumber(Integer.parseInt(m.group(2))); fragment.setFlowcellId(m.group(3)); fragment.setLane(Integer.parseInt(m.group(4))); fragment.setTile(Integer.parseInt(m.group(5))); fragment.setXpos(Integer.parseInt(m.group(6))); fragment.setYpos(Integer.parseInt(m.group(7))); fragment.setRead(Integer.parseInt(m.group(8))); fragment.setFilterPassed("N".equals(m.group(9))); fragment.setControlNumber(Integer.parseInt(m.group(10))); fragment.setIndexSequence(m.group(11)); } return matches; }
private boolean scanIlluminaId(Text name, SequencedFragment fragment) { Matcher m = ILLUMINA_PATTERN.matcher(name.toString()); boolean matches = m.matches(); if (matches) { fragment.setInstrument(m.group(1)); fragment.setRunNumber(Integer.parseInt(m.group(2))); fragment.setFlowcellId(m.group(3)); fragment.setLane(Integer.parseInt(m.group(4))); fragment.setTile(Integer.parseInt(m.group(5))); fragment.setXpos(Integer.parseInt(m.group(6))); fragment.setYpos(Integer.parseInt(m.group(7))); fragment.setRead(Integer.parseInt(m.group(8))); fragment.setFilterPassed("N".equals(m.group(9))); fragment.setControlNumber(Integer.parseInt(m.group(10))); fragment.setIndexSequence(m.group(11)); } return matches; }
private boolean scanIlluminaId(Text name, SequencedFragment fragment) { Matcher m = ILLUMINA_PATTERN.matcher(name.toString()); boolean matches = m.matches(); if (matches) { fragment.setInstrument(m.group(1)); fragment.setRunNumber(Integer.parseInt(m.group(2))); fragment.setFlowcellId(m.group(3)); fragment.setLane(Integer.parseInt(m.group(4))); fragment.setTile(Integer.parseInt(m.group(5))); fragment.setXpos(Integer.parseInt(m.group(6))); fragment.setYpos(Integer.parseInt(m.group(7))); fragment.setRead(Integer.parseInt(m.group(8))); fragment.setFilterPassed("N".equals(m.group(9))); fragment.setControlNumber(Integer.parseInt(m.group(10))); fragment.setIndexSequence(m.group(11)); } return matches; }
fragment.setTile( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[3], fieldLengths[3])) ); fragment.setXpos( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[4], fieldLengths[4])) ); fragment.setYpos( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[5], fieldLengths[5])) ); fragment.setRead( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[7], fieldLengths[7])) ); fragment.setFilterPassed( line.getBytes()[fieldPositions[10]] != '0' );
fragment.setTile( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[3], fieldLengths[3])) ); fragment.setXpos( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[4], fieldLengths[4])) ); fragment.setYpos( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[5], fieldLengths[5])) ); fragment.setRead( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[7], fieldLengths[7])) ); fragment.setFilterPassed( line.getBytes()[fieldPositions[10]] != '0' );
fragment.setTile( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[3], fieldLengths[3])) ); fragment.setXpos( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[4], fieldLengths[4])) ); fragment.setYpos( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[5], fieldLengths[5])) ); fragment.setRead( Integer.parseInt(Text.decode(line.getBytes(), fieldPositions[7], fieldLengths[7])) ); fragment.setFilterPassed( line.getBytes()[fieldPositions[10]] != '0' );
@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); }
@Test public void testToString() { String seq = "AGTAGTAGTAGTAGTAGTAGTAGTAGTAGT"; String qual = "##############################"; frag.setSequence(new Text(seq)); frag.setQuality(new Text(qual)); frag.setInstrument("machine"); frag.setRunNumber(123); frag.setFlowcellId("flowcell"); frag.setLane(3); frag.setTile(1001); frag.setXpos(1234); frag.setYpos(4321); frag.setIndexSequence("CAT"); frag.setRead(1); assertEquals("machine\t123\tflowcell\t3\t1001\t1234\t4321\tCAT\t1\t" + seq + "\t" + qual + "\t1", frag.toString()); }