@Test
public void testSamReaderFromURL() throws IOException {
final String samFilePath = new File(TEST_DATA_DIR, "unsorted.sam").getAbsolutePath();
final URL samURL = new URL("file://" + samFilePath);
final SamReaderFactory factory =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
final SamReader reader = factory.open(SamInputResource.of(samURL));
Assert.assertEquals(countRecords(reader), 10);
}
@Test
public void testSamReaderFromSeekableStream() throws IOException {
// even though a SAM isn't indexable, make sure we can open one
// using a seekable stream
final File samFile = new File(TEST_DATA_DIR, "unsorted.sam");
final SamReaderFactory factory =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
final SamReader reader = factory.open(SamInputResource.of(new SeekableFileStream(samFile)));
Assert.assertEquals(countRecords(reader), 10);
}
@Test(expectedExceptions = SAMFormatException.class)
public void testSamReaderFromMalformedSeekableStream() throws IOException {
// use a bogus (.bai file) to force SamReaderFactory to fall through to the
// fallback code that assumes a SAM File when it can't determine the
// format of the input, to ensure that it results in a SAMFormatException
final File samFile = new File(TEST_DATA_DIR, "cram_with_bai_index.cram.bai");
final SamReaderFactory factory =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
final SamReader reader = factory.open(SamInputResource.of(new SeekableFileStream(samFile)));
countRecords(reader);
}
public SamReader getSamReader(ResourceLocator locator, boolean requireIndex) throws IOException {
if (requireIndex) {
final SamReaderFactory factory =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
SeekableStream indexStream = getIndexStream(locator.getBamIndexPath());
this.indexed = true;
SeekableStream ss =
new IGVSeekableBufferedStream(
IGVSeekableStreamFactory.getInstance().getStreamFor(url), 128000);
SamInputResource resource = SamInputResource.of(ss).index(indexStream);
return factory.open(resource);
} else {
InputStream is = HttpUtils.getInstance().openConnectionStream(url);
return new SAMFileReader(new BufferedInputStream(is));
}
}
@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);
}
private void getCRAMReaderFromInputResource(
final BiFunction<URL, URL, SamInputResource> getInputResource,
final boolean hasIndex,
final int expectedCount)
throws IOException {
final String cramFilePath =
new File(TEST_DATA_DIR, "cram_with_bai_index.cram").getAbsolutePath();
final String cramIndexPath =
new File(TEST_DATA_DIR, "cram_with_bai_index.cram.bai").getAbsolutePath();
final URL cramURL = new URL("file://" + cramFilePath);
final URL indexURL = new URL("file://" + cramIndexPath);
final SamReaderFactory factory =
SamReaderFactory.makeDefault()
.referenceSource(new ReferenceSource(new File(TEST_DATA_DIR, "hg19mini.fasta")))
.validationStringency(ValidationStringency.SILENT);
final SamReader reader = factory.open(getInputResource.apply(cramURL, indexURL));
int count =
hasIndex
? countRecordsInQueryInterval(reader, new QueryInterval(1, 10, 1000))
: countRecords(reader);
Assert.assertEquals(count, expectedCount);
}
