@Test
public void inputResourceFromStringTest() throws IOException {
Assert.assertEquals(
SamInputResource.of("http://test.url").data().type(), InputResource.Type.URL);
Assert.assertEquals(
SamInputResource.of("https://test.url").data().type(), InputResource.Type.URL);
Assert.assertEquals(
SamInputResource.of("ftp://test.url").data().type(), InputResource.Type.URL);
Assert.assertEquals(SamInputResource.of("/a/b/c").data().type(), InputResource.Type.FILE);
}
@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();
}
@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 = RuntimeIOException.class)
public void testCRAMReaderFromURLBadIndexFile() throws IOException {
// deliberately specify a bad index file to ensure we get an IOException
getCRAMReaderFromInputResource(
(cramURL, indexURL) -> {
return SamInputResource.of(cramURL).index(new File("nonexistent.bai"));
},
true,
3);
}
@Test
public void testCRAMReaderFromURLNoIndexFile() throws IOException {
// get just a CRAM reader (no index) from an URL-backed resource
getCRAMReaderFromInputResource(
(cramURL, indexURL) -> {
return SamInputResource.of(cramURL);
},
false,
11);
}
@Test
public void testCRAMReaderFromURL() throws IOException {
// get a CRAM reader with an index from a URL-backed resource
getCRAMReaderFromInputResource(
(cramURL, indexURL) -> {
return SamInputResource.of(cramURL).index(indexURL);
},
true,
3);
}
@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);
}
@Test
public void testCRAMReaderFromURLStream() throws IOException {
// get a CRAM reader with an index from a stream-backed resource created from a URL
getCRAMReaderFromInputResource(
(cramURL, indexURL) -> {
try {
ISeekableStreamFactory streamFactory = SeekableStreamFactory.getInstance();
return SamInputResource.of(streamFactory.getStreamFor(cramURL))
.index(streamFactory.getStreamFor(indexURL));
} catch (IOException e) {
throw new RuntimeIOException(e);
}
},
true,
3);
}
@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();
}
}
