private boolean listContainsFeature(List<Feature> featureList, Feature feature) {
for (Feature listFeature : featureList) {
if ((feature.getChr().equals(listFeature.getChr()))
&& (feature.getStart() == listFeature.getStart())
&& (feature.getEnd() == listFeature.getEnd())) {
return true;
}
}
return false;
}
/**
* Test loading a session with a bedtools analysis track
*
* @throws Exception
*/
@Test
public void testLoadBedtools_Subtract() throws Exception {
String toolPath = "/usr/local/bin/bedtools";
boolean haveTool = PluginSpecReader.isToolPathValid(toolPath);
Assume.assumeTrue(haveTool);
String sessionPath = TestUtils.DATA_DIR + "sessions/GSM_bedtools_subtract.xml";
rewriteRestoreSession(sessionPath);
String trackAname = "GSM1004654_100k.bed";
String trackBname = "GSM1004654_10k.bed";
String analId = "BEDTools Remove/Subtract";
FeatureTrack analTrack = null, trackA = null, trackB = null;
for (Track track : IGV.getInstance().getAllTracks()) {
if (track.getId().equals(analId)) {
analTrack = (FeatureTrack) track;
} else if (track.getName().equals(trackAname)) {
trackA = (FeatureTrack) track;
} else if (track.getName().equals(trackBname)) {
trackB = (FeatureTrack) track;
}
}
String chr = "chr2";
int start = 177932002;
int end = 180561093;
List<Feature> aFeatures = trackA.getFeatures(chr, start, end);
List<Feature> bFeatures = trackB.getFeatures(chr, start, end);
List<Feature> analFeatures = analTrack.getFeatures(chr, start, end);
// Fairly coarse check, these actually might not exactly be true
// due to splitting of exons
int checked = 0;
for (Feature afeat : analFeatures) {
if (afeat.getStart() < start || afeat.getStart() > end) continue;
// This particular feature splits funny, it's not a bug, at least not with IGV
if (afeat.getStart() == 178625608) continue;
assertTrue(listContainsFeature(aFeatures, afeat));
assertFalse(listContainsFeature(bFeatures, afeat));
checked++;
}
assert checked > 0;
}