public SeekingBAMFileReader(final SamInputResource resource, final boolean eagerDecode, final ValidationStringency validationStringency, final SAMRecordFactory factory, long offset) throws IOException { super(resource.data().asUnbufferedSeekableStream(), (SeekableStream)null, eagerDecode, validationStringency, factory); this.offset = offset; this.stream = resource.data().asUnbufferedSeekableStream(); }
public SeekingBAMFileReader(final SamInputResource resource, final boolean eagerDecode, final ValidationStringency validationStringency, final SAMRecordFactory factory, long offset) throws IOException { super(resource.data().asUnbufferedSeekableStream(), (SeekableStream)null, eagerDecode, validationStringency, factory); this.offset = offset; this.stream = resource.data().asUnbufferedSeekableStream(); }
@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 public void testWrappersAreAccessed() throws Exception { Path path = Paths.get(localBam); Path indexPath = Paths.get(localBam + ".bai"); HashMap<String, Boolean> fired = new HashMap<>(); Function<SeekableByteChannel, SeekableByteChannel> wrapData = (SeekableByteChannel in) -> { fired.put("data", true); return in; }; Function<SeekableByteChannel, SeekableByteChannel> wrapIndex = (SeekableByteChannel in) -> { fired.put("index", true); return in; }; SamInputResource in = SamInputResource.of(path, wrapData); in.index(indexPath, wrapIndex); InputResource indexResource = in.indexMaybe(); Assert.assertNotNull(indexResource); Assert.assertFalse(fired.containsKey("data")); Assert.assertFalse(fired.containsKey("index")); indexResource.asUnbufferedSeekableStream(); Assert.assertFalse(fired.containsKey("data")); Assert.assertTrue(fired.containsKey("index")); in.data().asUnbufferedSeekableStream(); Assert.assertTrue(fired.containsKey("data")); Assert.assertTrue(fired.containsKey("index")); }
final SamReader.PrimitiveSamReader primitiveSamReader; try { final InputResource data = resource.data(); final InputResource indexMaybe = resource.indexMaybe(); final boolean indexDefined = indexMaybe != null;
final SamReader.PrimitiveSamReader primitiveSamReader; try { final InputResource data = resource.data(); final InputResource indexMaybe = resource.indexMaybe(); final boolean indexDefined = indexMaybe != null;
final SamReader.PrimitiveSamReader primitiveSamReader; try { final InputResource data = resource.data(); final InputResource indexMaybe = resource.indexMaybe(); final boolean indexDefined = indexMaybe != null;