@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());
}
}
