@Override public SAMReadGroupRecord createRecord(final String id, final SAMReadGroupRecord srcReadGroupRecord) { return new SAMReadGroupRecord(id, srcReadGroupRecord); } };
@Override public SAMReadGroupRecord createRecord(final String id, final SAMReadGroupRecord srcReadGroupRecord) { return new SAMReadGroupRecord(id, srcReadGroupRecord); } };
public SAMReadGroupRecord createRecord(final String id, final SAMReadGroupRecord srcReadGroupRecord) { return new SAMReadGroupRecord(id, srcReadGroupRecord); } };
@Test(expectedExceptions = {PicardException.class}) public void testAssertAllReadGroupsMappedFailure() { final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("rg1"); final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("rg2"); final SAMReadGroupRecord rg3 = new SAMReadGroupRecord("rg3"); final Map<String, File> outputMap = new HashMap<String, File>(); outputMap.put("rg1", new File("/foo/bar/rg1.bam")); outputMap.put("rg2", new File("/foo/bar/rg2.bam")); RevertSam.ValidationUtil.assertAllReadGroupsMapped(outputMap, Arrays.asList(rg1, rg2, rg3)); }
@Test public void testFilePathsWithoutMapFile() { final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("rg1"); final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("rg2"); final Map<String, File> outputMap = RevertSam.createOutputMap(null, new File("/foo/bar"), ".bam", Arrays.asList(rg1, rg2)); Assert.assertEquals(outputMap.get("rg1"), new File("/foo/bar/rg1.bam")); Assert.assertEquals(outputMap.get("rg2"), new File("/foo/bar/rg2.bam")); }
private SAMReadGroupRecord createRG(String name) { SAMReadGroupRecord rg = new SAMReadGroupRecord(name); rg.setPlatform(rgPlatform.getDefaultPlatform()); rg.setSample(name); return rg; }
@Test public void testAssertAllReadGroupsMappedSuccess() { final SAMReadGroupRecord rg1 = new SAMReadGroupRecord("rg1"); final SAMReadGroupRecord rg2 = new SAMReadGroupRecord("rg2"); final Map<String, File> outputMap = new HashMap<String, File>(); outputMap.put("rg1", new File("/foo/bar/rg1.bam")); outputMap.put("rg2", new File("/foo/bar/rg2.bam")); RevertSam.ValidationUtil.assertAllReadGroupsMapped(outputMap, Arrays.asList(rg1, rg2)); RevertSam.ValidationUtil.assertAllReadGroupsMapped(outputMap, Arrays.asList(rg1)); RevertSam.ValidationUtil.assertAllReadGroupsMapped(outputMap, Arrays.asList(rg2)); }
@Test public void testReadGroupIdGetters() throws Exception { final SAMReadGroupRecord rg = new SAMReadGroupRecord("rg1"); Assert.assertEquals(rg.getId(), "rg1"); Assert.assertEquals(rg.getReadGroupId(), "rg1"); }
private SAMReadGroupRecord createSAMReadGroupRecord(String id) { SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord(id); readGroupRecord.setAttribute(SAMTag.SM.name(), Double.toString(Math.random())); return readGroupRecord; }
@Test public void testSetNonIso8601Date() throws Exception { final SAMReadGroupRecord rg = new SAMReadGroupRecord("rg1"); // set not ISO 8601 date final Date date = new Date(); rg.setRunDate(date); // and assert that it is correctly wrapped Assert.assertEquals(rg.getRunDate(), new Iso8601Date(date)); }
@Test(expectedExceptions = UserException.class) public void testGetSAMFileMissingReadGroupsSamples() { final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(); final SAMReadGroupRecord samGroup = new SAMReadGroupRecord("id"); final List<SAMReadGroupRecord> list = new ArrayList<>(Arrays.asList(samGroup)); header.setReadGroups(list); ReadUtils.getSAMFileSamples(header); } }
@Override AbstractSAMHeaderRecord newGroup(String id) { SAMReadGroupRecord group = new SAMReadGroupRecord(id); group.setAttribute(SAMTag.SM.name(), id); return group; }
@Test(dataProvider = "getBarcodes") public void testGetAndSetBarcodes(List<String> barcodes, String encoded){ final SAMReadGroupRecord readGroup = new SAMReadGroupRecord("ReadGroup"); Assert.assertNull(readGroup.getBarcodes()); Assert.assertNull(readGroup.getAttribute(SAMReadGroupRecord.BARCODE_TAG)); readGroup.setBarcodes(barcodes); Assert.assertEquals(readGroup.getBarcodes(), barcodes); Assert.assertEquals(readGroup.getAttribute(SAMReadGroupRecord.BARCODE_TAG), encoded); } }
@DataProvider(name="UsualSuspects") public Object[][] createData() { final SAMReadGroupRecord left = new SAMReadGroupRecord("left"); left.setPlatformUnit("left.1"); left.setLibrary("library"); final SAMReadGroupRecord right = new SAMReadGroupRecord("right"); right.setPlatformUnit("right.1"); right.setLibrary("library"); right.setDescription("description"); return new Object[][] {{ left, right }}; }
@Test public void testGetSAMString() { SAMReadGroupRecord r = new SAMReadGroupRecord("rg1"); r.setSample("mysample"); r.setPlatform("ILLUMINA"); r.setDescription("my description"); Assert.assertEquals("@RG\tID:rg1\tSM:mysample\tPL:ILLUMINA\tDS:my description", r.getSAMString()); }
@Test() public void testPLFromReadWithRGButNoPL() { final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); final String rgID = "ID"; final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID); header.addReadGroup(rg); final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10); read.setAttribute("RG", rgID); Assert.assertEquals(NGSPlatform.fromRead(read), NGSPlatform.UNKNOWN); }
/** * A unit test that creates an artificial read for testing some code that uses reads */ @Test(dataProvider = "TestMappings") public void testPLFromReadWithRG(final String plField, final NGSPlatform expected) { final SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(seq.getSequenceDictionary()); final String rgID = "ID"; final SAMReadGroupRecord rg = new SAMReadGroupRecord(rgID); if ( plField != null ) rg.setPlatform(plField); header.addReadGroup(rg); final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "myRead", 0, 1, 10); read.setAttribute("RG", rgID); Assert.assertEquals(NGSPlatform.fromRead(read), expected); }
private SAMFileHeader createSAMHeader(SAMFileHeader.SortOrder sortOrder) { final SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(sortOrder); header.addSequence(new SAMSequenceRecord("chr1", 123)); SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord("1"); header.addReadGroup(readGroupRecord); return header; }
private SAMFileHeader createSAMHeader(SAMFileHeader.SortOrder sortOrder) { final SAMFileHeader header = new SAMFileHeader(); header.setSortOrder(sortOrder); header.addSequence(new SAMSequenceRecord("chr1", 123)); header.addSequence(new SAMSequenceRecord("chr2", 123)); SAMReadGroupRecord readGroupRecord = new SAMReadGroupRecord("1"); header.addReadGroup(readGroupRecord); return header; }
private SAMFileWriterFactory createWriterFactoryWithOptions(SAMFileHeader header) { final SAMFileWriterFactory factory = new SAMFileWriterFactory(); factory.setCreateIndex(true); factory.setCreateMd5File(true); // index only created if coordinate sorted header.setSortOrder(SAMFileHeader.SortOrder.coordinate); header.addSequence(new SAMSequenceRecord("chr1", 123)); header.addReadGroup(new SAMReadGroupRecord("1")); return factory; }