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 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());
}
}
/**
* 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);
}