Esempio n. 1
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  @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);
    }
  }
Esempio n. 2
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 // 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();
 }
Esempio n. 3
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  @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");
  }