@Test
public void testVCFHeaderSerialization() throws Exception {
final VCFFileReader reader =
new VCFFileReader(new File("testdata/htsjdk/variant/HiSeq.10000.vcf"), false);
final VCFHeader originalHeader = reader.getFileHeader();
reader.close();
final VCFHeader deserializedHeader = TestUtil.serializeAndDeserialize(originalHeader);
Assert.assertEquals(
deserializedHeader.getMetaDataInInputOrder(),
originalHeader.getMetaDataInInputOrder(),
"Header metadata does not match before/after serialization");
Assert.assertEquals(
deserializedHeader.getContigLines(),
originalHeader.getContigLines(),
"Contig header lines do not match before/after serialization");
Assert.assertEquals(
deserializedHeader.getFilterLines(),
originalHeader.getFilterLines(),
"Filter header lines do not match before/after serialization");
Assert.assertEquals(
deserializedHeader.getFormatHeaderLines(),
originalHeader.getFormatHeaderLines(),
"Format header lines do not match before/after serialization");
Assert.assertEquals(
deserializedHeader.getIDHeaderLines(),
originalHeader.getIDHeaderLines(),
"ID header lines do not match before/after serialization");
Assert.assertEquals(
deserializedHeader.getInfoHeaderLines(),
originalHeader.getInfoHeaderLines(),
"Info header lines do not match before/after serialization");
Assert.assertEquals(
deserializedHeader.getOtherHeaderLines(),
originalHeader.getOtherHeaderLines(),
"Other header lines do not match before/after serialization");
Assert.assertEquals(
deserializedHeader.getGenotypeSamples(),
originalHeader.getGenotypeSamples(),
"Genotype samples not the same before/after serialization");
Assert.assertEquals(
deserializedHeader.samplesWereAlreadySorted(),
originalHeader.samplesWereAlreadySorted(),
"Sortedness of samples not the same before/after serialization");
Assert.assertEquals(
deserializedHeader.getSampleNamesInOrder(),
originalHeader.getSampleNamesInOrder(),
"Sorted list of sample names in header not the same before/after serialization");
Assert.assertEquals(
deserializedHeader.getSampleNameToOffset(),
originalHeader.getSampleNameToOffset(),
"Sample name to offset map not the same before/after serialization");
Assert.assertEquals(
deserializedHeader.toString(),
originalHeader.toString(),
"String representation of header not the same before/after serialization");
}
@Test(dataProvider = "testOpticalDuplicateDetectionDataProvider")
public void testOpticalDuplicateDetection(
final File sam, final long expectedNumOpticalDuplicates) {
final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
outputDir.deleteOnExit();
final File outputSam = new File(outputDir, TEST_BASE_NAME + ".sam");
outputSam.deleteOnExit();
final File metricsFile = new File(outputDir, TEST_BASE_NAME + ".duplicate_metrics");
metricsFile.deleteOnExit();
// Run MarkDuplicates, merging the 3 input files, and either enabling or suppressing PG header
// record creation according to suppressPg.
final MarkDuplicates markDuplicates = new MarkDuplicates();
markDuplicates.setupOpticalDuplicateFinder();
markDuplicates.INPUT = CollectionUtil.makeList(sam.getAbsolutePath());
markDuplicates.OUTPUT = outputSam;
markDuplicates.METRICS_FILE = metricsFile;
markDuplicates.TMP_DIR = CollectionUtil.makeList(outputDir);
// Needed to suppress calling CommandLineProgram.getVersion(), which doesn't work for code not
// in a jar
markDuplicates.PROGRAM_RECORD_ID = null;
Assert.assertEquals(markDuplicates.doWork(), 0);
Assert.assertEquals(markDuplicates.numOpticalDuplicates(), expectedNumOpticalDuplicates);
TestUtil.recursiveDelete(outputDir);
}
/**
* Test that PG header records are created & chained appropriately (or not created), and that the
* PG record chains are as expected. MarkDuplicates is used both to merge and to mark dupes in
* this case.
*
* @param suppressPg If true, do not create PG header record.
* @param expectedPnVnByReadName For each read, info about the expect chain of PG records.
*/
@Test(dataProvider = "pgRecordChainingTest")
public void pgRecordChainingTest(
final boolean suppressPg, final Map<String, List<ExpectedPnAndVn>> expectedPnVnByReadName) {
final File outputDir = IOUtil.createTempDir(TEST_BASE_NAME + ".", ".tmp");
outputDir.deleteOnExit();
try {
// Run MarkDuplicates, merging the 3 input files, and either enabling or suppressing PG header
// record creation according to suppressPg.
final MarkDuplicates markDuplicates = new MarkDuplicates();
final ArrayList<String> args = new ArrayList<String>();
for (int i = 1; i <= 3; ++i) {
args.add("INPUT=" + new File(TEST_DATA_DIR, "merge" + i + ".sam").getAbsolutePath());
}
final File outputSam = new File(outputDir, TEST_BASE_NAME + ".sam");
args.add("OUTPUT=" + outputSam.getAbsolutePath());
args.add(
"METRICS_FILE="
+ new File(outputDir, TEST_BASE_NAME + ".duplicate_metrics").getAbsolutePath());
if (suppressPg) args.add("PROGRAM_RECORD_ID=null");
// I generally prefer to call doWork rather than invoking the argument parser, but it is
// necessary
// in this case to initialize the command line.
// Note that for the unit test, version won't come through because it is obtained through jar
// manifest, and unit test doesn't run code from a jar.
Assert.assertEquals(markDuplicates.instanceMain(args.toArray(new String[args.size()])), 0);
// Read the MarkDuplicates output file, and get the PG ID for each read. In this particular
// test,
// the PG ID should be the same for both ends of a pair.
final SamReader reader = SamReaderFactory.makeDefault().open(outputSam);
final Map<String, String> pgIdForReadName = new HashMap<String, String>();
for (final SAMRecord rec : reader) {
final String existingPgId = pgIdForReadName.get(rec.getReadName());
final String thisPgId = rec.getStringAttribute(SAMTag.PG.name());
if (existingPgId != null) {
Assert.assertEquals(thisPgId, existingPgId);
} else {
pgIdForReadName.put(rec.getReadName(), thisPgId);
}
}
final SAMFileHeader header = reader.getFileHeader();
CloserUtil.close(reader);
// Confirm that for each read name, the chain of PG records contains exactly the number that
// is expected,
// and that values in the PG chain are as expected.
for (final Map.Entry<String, List<ExpectedPnAndVn>> entry :
expectedPnVnByReadName.entrySet()) {
final String readName = entry.getKey();
final List<ExpectedPnAndVn> expectedList = entry.getValue();
String pgId = pgIdForReadName.get(readName);
for (final ExpectedPnAndVn expected : expectedList) {
final SAMProgramRecord programRecord = header.getProgramRecord(pgId);
if (expected.expectedPn != null)
Assert.assertEquals(programRecord.getProgramName(), expected.expectedPn);
if (expected.expectedVn != null)
Assert.assertEquals(programRecord.getProgramVersion(), expected.expectedVn);
pgId = programRecord.getPreviousProgramGroupId();
}
Assert.assertNull(pgId);
}
} finally {
TestUtil.recursiveDelete(outputDir);
}
}