Exemplo n.º 1
0
 @Test(dataProvider = "variousFormatReaderTestCases")
 public void variousFormatReaderTest(final String inputFile) throws IOException {
   final File input = new File(TEST_DATA_DIR, inputFile);
   final SamReader reader = SamReaderFactory.makeDefault().open(input);
   for (final SAMRecord ignored : reader) {}
   reader.close();
 }
Exemplo n.º 2
0
  @Test(dataProvider = "composeAllPermutationsOfSamInputResource")
  public void queryInputResourcePermutation(final SamInputResource resource) throws IOException {
    final SamReader reader = SamReaderFactory.makeDefault().open(resource);
    LOG.info(String.format("Query from %s ...", resource));
    if (reader.hasIndex()) {
      final StopWatch stopWatch = new StopWatch();
      stopWatch.start();
      final SAMRecordIterator q1 = reader.query("chr1", 500000, 100000000, true);
      observedRecordOrdering1.add(Iterables.slurp(q1));
      q1.close();
      final SAMRecordIterator q20 = reader.query("chr20", 1, 1000000, true);
      observedRecordOrdering20.add(Iterables.slurp(q20));
      q20.close();
      final SAMRecordIterator q3 = reader.query("chr3", 1, 10000000, true);
      observedRecordOrdering3.add(Iterables.slurp(q3));
      q3.close();
      stopWatch.stop();
      LOG.info(String.format("Finished queries in %sms", stopWatch.getElapsedTime()));

      Assert.assertEquals(
          observedRecordOrdering1.size(), 1, "read different records for chromosome 1");
      Assert.assertEquals(
          observedRecordOrdering20.size(), 1, "read different records for chromosome 20");
      Assert.assertEquals(
          observedRecordOrdering3.size(), 1, "read different records for chromosome 3");
    } else if (resource.indexMaybe() != null) {
      LOG.warn("Resource has an index source, but is not indexed: " + resource);
    } else {
      LOG.info("Skipping query operation: no index.");
    }
    reader.close();
  }
Exemplo n.º 3
0
 // See https://github.com/samtools/htsjdk/issues/76
 @Test(dataProvider = "queryIntervalIssue76TestCases")
 public void queryIntervalIssue76(
     final String sequenceName, final int start, final int end, final int expectedCount)
     throws IOException {
   final File input = new File(TEST_DATA_DIR, "issue76.bam");
   final SamReader reader = SamReaderFactory.makeDefault().open(input);
   final QueryInterval interval =
       new QueryInterval(
           reader.getFileHeader().getSequence(sequenceName).getSequenceIndex(), start, end);
   Assert.assertEquals(countRecordsInQueryInterval(reader, interval), expectedCount);
   reader.close();
 }
Exemplo n.º 4
0
  @Test(dataProvider = "composeAllPermutationsOfSamInputResource")
  public void exhaustInputResourcePermutation(final SamInputResource resource) throws IOException {
    final SamReader reader = SamReaderFactory.makeDefault().open(resource);
    LOG.info(String.format("Reading from %s ...", resource));
    final List<SAMRecord> slurped = Iterables.slurp(reader);
    final SAMFileHeader fileHeader = reader.getFileHeader();
    reader.hasIndex();
    reader.indexing().hasBrowseableIndex();
    reader.close();

    /* Ensure all tests have read the same records in the same order or, if this is the first test, set it as the template. */
    observedHeaders.add(fileHeader);
    observedRecordOrdering.add(slurped);
    Assert.assertEquals(observedHeaders.size(), 1, "read different headers than other testcases");
    Assert.assertEquals(
        observedRecordOrdering.size(), 1, "read different records than other testcases");
  }
Exemplo n.º 5
0
  @Test
  public void openPath() throws IOException {
    final Path path = localBam.toPath();
    final List<SAMRecord> records;
    final SAMFileHeader fileHeader;
    try (final SamReader reader = SamReaderFactory.makeDefault().open(path)) {
      LOG.info(String.format("Reading from %s ...", path));
      records = Iterables.slurp(reader);
      fileHeader = reader.getFileHeader();
      reader.close();
    }

    try (final SamReader fileReader = SamReaderFactory.makeDefault().open(localBam)) {
      final List<SAMRecord> expectedRecords = Iterables.slurp(fileReader);
      final SAMFileHeader expectedFileHeader = fileReader.getFileHeader();
      Assert.assertEquals(records, expectedRecords);
      Assert.assertEquals(fileHeader, expectedFileHeader);
    }
  }
Exemplo n.º 6
0
  @Test(dataProvider = "variousFormatReaderTestCases")
  public void samRecordFactoryTest(final String inputFile) throws IOException {
    final File input = new File(TEST_DATA_DIR, inputFile);

    final SAMRecordFactoryTester recordFactory = new SAMRecordFactoryTester();
    final SamReaderFactory readerFactory =
        SamReaderFactory.makeDefault().samRecordFactory(recordFactory);
    final SamReader reader = readerFactory.open(input);

    int i = 0;
    for (final SAMRecord ignored : reader) {
      ++i;
    }
    reader.close();

    Assert.assertTrue(i > 0);
    if (inputFile.endsWith(".sam") || inputFile.endsWith(".sam.gz"))
      Assert.assertEquals(recordFactory.samRecordsCreated, i);
    else if (inputFile.endsWith(".bam")) Assert.assertEquals(recordFactory.bamRecordsCreated, i);
  }
Exemplo n.º 7
0
  @Test
  public void customReaderFactoryTest() throws IOException {
    try {
      CustomReaderFactory.setInstance(
          new CustomReaderFactory(
              "https://www.googleapis.com/genomics/v1beta/reads/,"
                  + "htsjdk.samtools.SamReaderFactoryTest$TestReaderFactory"));
      final SamReader reader =
          SamReaderFactory.makeDefault()
              .open(
                  SamInputResource.of(
                      "https://www.googleapis.com/genomics/v1beta/reads/?uncompressed.sam"));
      int i = 0;
      for (@SuppressWarnings("unused") final SAMRecord ignored : reader) {
        ++i;
      }
      reader.close();

      Assert.assertTrue(i > 0);
    } finally {
      CustomReaderFactory.resetToDefaultInstance();
    }
  }