@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
public void testLoadGFFAliasedChrs() throws Exception {
String filepath = TestUtils.DATA_DIR + "gff/aliased.unsorted.gff";
Genome genome =
IgvTools.loadGenome(TestUtils.DATA_DIR + "genomes/hg18_truncated_aliased.genome");
List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
assertEquals(1, tracks.size());
FeatureTrack track = (FeatureTrack) tracks.get(0);
assertEquals("aliased.unsorted.gff", track.getName());
List<Feature> features = track.getFeatures("chr1", 0, Integer.MAX_VALUE);
assertEquals(56, features.size());
features = track.getFeatures("chr5", 0, Integer.MAX_VALUE);
assertEquals(16, features.size());
// Non-aliased
features = track.getFeatures("NC_007072.3", 0, Integer.MAX_VALUE);
assertEquals(30, features.size());
}
@Test
public void testLoadGFF() throws Exception {
String filepath = TestUtils.DATA_DIR + "gff/simfeatures.gff3";
List<Track> tracks = trackLoader.load(new ResourceLocator(filepath), genome);
assertEquals(1, tracks.size());
FeatureTrack track = (FeatureTrack) tracks.get(0);
assertEquals("notmeaningful", track.getName());
List<Feature> features = track.getFeatures("chr1", 0, Integer.MAX_VALUE);
assertEquals(2, features.size());
IGVFeature feat0 = (IGVFeature) features.get(0);
IGVFeature feat1 = (IGVFeature) features.get(1);
assertEquals(707 - 1, feat0.getStart());
assertEquals(943, feat0.getEnd());
assertEquals(7563 - 1, feat1.getStart());
assertEquals(7938, feat1.getEnd());
}