@Override
protected Index doInBackground() throws Exception {
int binSize = IgvTools.LINEAR_BIN_SIZE;
FeatureCodec codec =
CodecFactory.getCodec(
file.getAbsolutePath(), GenomeManager.getInstance().getCurrentGenome());
if (codec != null) {
try {
Index index = IndexFactory.createLinearIndex(file, codec, binSize);
if (index != null) {
IgvTools.writeTribbleIndex(index, idxFile.getAbsolutePath());
}
return index;
} catch (TribbleException.MalformedFeatureFile e) {
StringBuffer buf = new StringBuffer();
buf.append("<html>Files must be sorted by start position prior to indexing.<br>");
buf.append(e.getMessage());
buf.append(
"<br><br>Note: igvtools can be used to sort the file, select \"File > Run igvtools...\".");
MessageUtils.showMessage(buf.toString());
}
} else {
throw new DataLoadException("Unknown File Type", file.getAbsolutePath());
}
return null;
}
@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());
}