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.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' );
@Test public void testNullFilter() throws IOException { fragment.setFilterPassed(null); writer.write(null, fragment); writer.close(null); String[] lines = new String(outputBuffer.toByteArray(), "US-ASCII").split("\n"); assertEquals(4, lines.length); String idLine = lines[0]; assertTrue(idLine.startsWith("@")); fragment.setFilterPassed(true); // when filter not available then it passes compareMetadata(fragment, idLine); }
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.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' );
@Test public void testEqualsFilterPassed() { frag.setFilterPassed(false); assertFalse( frag.equals(frag2) ); frag2.setFilterPassed(false); assertTrue( frag.equals(frag2) ); }
@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); }