@Test
public void testBedAndBigBed() throws Exception {
String bedPath = TestUtils.DATA_DIR + "bed/Unigene.sample.nolong.bed";
String bigBedPath = TestUtils.DATA_DIR + "bed/Unigene.sample.nolong.bigbed";
File bigBedFile = new File(bigBedPath);
// Need to index so query of bed file is accurate
TestUtils.createIndex(bedPath);
List<Track> bedtracks = tstLoadFi(bedPath, 1, false);
List<Track> bigBedtracks = tstLoadFi(bigBedPath, 1, false);
String chr = "chr2";
int start = 178711404 - 1;
int end = 179189619 + 1;
FeatureTrack bedTrack = (FeatureTrack) bedtracks.get(0);
FeatureTrack bigBedTrack = (FeatureTrack) bigBedtracks.get(0);
// Multiple trials because we're concerned about file open/close issues
int trials = 10;
for (int ii = 0; ii < trials; ii++) {
int strt = start + ii;
List<Feature> bedFeatures = bedTrack.getFeatures(chr, strt, end);
List<Feature> bigBedFeatures = bigBedTrack.getFeatures(chr, strt, end);
TestUtils.assertFeatureListsEqual(bedFeatures.iterator(), bigBedFeatures.iterator());
// NOT FOOLPROOF
assertTrue(bigBedFile.canWrite());
}
}
@BeforeClass
public static void setUpClass() throws Exception {
assumeNotHeadless();
TestUtils.setUpTestEnvironment();
igv = startGUI();
TestUtils.setAllNames(igv, true);
}
@Before
public void setUp() throws Exception {
igv.newSession();
IGV.getMainFrame().requestFocus();
TestUtils.resetPrefsFile();
TestUtils.resetTestUserDefinedGenomes();
IGV.getInstance().getContentPane().getCommandBar().refreshGenomeListComboBox();
}
static List<Track> tstLoadFi(
TrackLoader trackLoader,
String filepath,
Integer expected_tracks,
Genome genome,
boolean makeIndex)
throws Exception {
ResourceLocator locator = new ResourceLocator(filepath);
// Try creating an index
// UI would ask for confirmation
if (makeIndex) {
try {
TestUtils.createIndex(filepath);
} catch (Exception e) {
}
}
List<Track> tracks = trackLoader.load(locator, genome);
if (expected_tracks != null) {
assertEquals(expected_tracks.intValue(), tracks.size());
if (expected_tracks == 0) {
return tracks;
}
}
Track track = tracks.get(0);
assertEquals(locator, track.getResourceLocator());
return tracks;
}
@Test
public void testEncodeDecode() throws Exception {
String testFile = TestUtils.DATA_DIR + "sam/NA12878.muc1.test.sam";
SAMReader reader = new SAMReader(testFile);
Iterator<PicardAlignment> inputAlignmentIterator = reader.iterator();
ArrayList<PicardAlignment> inputAlignmentList = new ArrayList<PicardAlignment>();
while (inputAlignmentIterator.hasNext()) {
PicardAlignment al = inputAlignmentIterator.next();
inputAlignmentList.add(al);
}
ByteArrayOutputStream bos = new ByteArrayOutputStream();
FeatureEncoder<PicardAlignment> alignmentEncoder = new SamAlignmentEncoder();
alignmentEncoder.encodeAll(bos, reader.iterator());
ByteArrayInputStream bis = new ByteArrayInputStream(bos.toByteArray());
FeatureDecoder<PicardAlignment> alignmentDecoder = new AlignmentDecoder();
Iterator<PicardAlignment> decodedAlignments = alignmentDecoder.decodeAll(bis, false);
int ind = 0;
while (decodedAlignments.hasNext()) {
Alignment act = decodedAlignments.next();
Alignment exp = inputAlignmentList.get(ind++);
TestUtils.assertFeaturesEqual(exp, act);
assertEquals(exp.getCigarString(), act.getCigarString());
}
assertEquals("Different number of alignments read in as out", inputAlignmentList.size(), ind);
}
@Test
public void testLoadDataSourceTrack() throws Exception {
String path = TestUtils.DATA_DIR + "sessions/tdf_session.xml";
rewriteRestoreSession(path);
DataSourceTrack track = (DataSourceTrack) IGV.getInstance().getAllTracks().get(0);
assertEquals(true, TestUtils.runMethod(track, "getNormalize"));
assertEquals("NA12878.SLX.egfr.sam.tdf", track.getName());
}
/**
* Test that we properly load a vcf file, even though the extension is upper-case. IGV-2012
*
* @throws Exception
*/
@Test
public void testLoadVCFUpperCase() throws Exception {
String filepath = TestUtils.DATA_DIR + "vcf/HC_MOD_CAPS.VCF";
ResourceLocator locator = new ResourceLocator(filepath);
TestUtils.createIndex(filepath);
List<Track> tracks = trackLoader.load(locator, genome);
assertEquals(1, tracks.size());
assertTrue("VCF file loaded incorrect track type", tracks.get(0) instanceof VariantTrack);
}
@Test
public void testLoadBEDtxt() throws Exception {
String filepath = TestUtils.DATA_DIR + "bed/intervalTest.bed.txt";
TestUtils.createIndex(filepath);
tstLoadFi(filepath, 1, true);
}
public void tstFilesHeadless(String[] filenames, boolean tryIndex) throws Exception {
Genome genome = TestUtils.loadGenome();
for (String finame : filenames) {
tstLoadFi(TestUtils.DATA_DIR + finame, null, genome, tryIndex);
}
}
private List<Track> tstLoadFi(String filepath, Integer expected_tracks, boolean makeIndex)
throws Exception {
Genome genome = TestUtils.loadGenome();
return tstLoadFi(filepath, expected_tracks, genome, makeIndex);
}
@After
public void tearDown() throws Exception {
TestUtils.resetPrefsFile();
TestUtils.resetTestUserDefinedGenomes();
}
@AfterClass
public static void tearDownClass() throws Exception {
TestUtils.clearOutputDir();
stopGUI();
igv = null;
}
protected static String rewriteRestoreSession(String sessionPath) throws Exception {
sessionPath = (TestUtils.replaceTestPaths(new File(sessionPath))).getAbsolutePath();
IGV.getInstance().doRestoreSession(sessionPath, null, false);
return sessionPath;
}
/**
* Get render options of the track, reflectively so we don't need to alter access controls
*
* @param track
* @return
* @throws Exception
*/
private AlignmentTrack.RenderOptions getRenderOptions(Track track) throws Exception {
Object result = TestUtils.getField(track, "renderOptions");
return (AlignmentTrack.RenderOptions) result;
}
