public TDFDataset getDataset(String chr, int zoom, WindowFunction windowFunction) { // Version 1 only had mean String wf = getVersion() < 2 ? "" : "/" + windowFunction.toString(); String zoomString = chr.equals(Globals.CHR_ALL) ? "0" : String.valueOf(zoom); String dsName = "/" + chr + "/z" + zoomString + wf; TDFDataset ds = getDataset(dsName); return ds; }
public TDFDataset getDataset(String chr, int zoom, WindowFunction windowFunction) { // Version 1 only had mean String wf = getVersion() < 2 ? "" : "/" + windowFunction.toString(); String dsName = "/" + chr + "/z" + zoom + wf; TDFDataset ds = getDataset(dsName); return ds; }
System.out.println("Version: " + reader.getVersion()); System.out.println("Window Functions"); for (WindowFunction wf : reader.getWindowFunctions()) {
if (reader.getVersion() >= 4) {
/** * IGV-1417 and/or IGV-1421 - error reading a version 1 file (error thrown in header) */ @Test public void test_IGV1417() { String tdfFile = "http://data.broadinstitute.org/igvdata/annotations/hg18/conservation/pi.ewig.tdf"; TDFReader reader = TDFReader.getReader(tdfFile); assertEquals(1, reader.getVersion()); }
@Test public void test_v3() { String tdfFile = "http://data.broadinstitute.org/igvdata/test/tdf/NA12878.pilot2.454.bam.tdf"; TDFReader reader = TDFReader.getReader(tdfFile); assertEquals(3, reader.getVersion()); }
@Test public void testReader() throws Exception { String url = "http://data.broadinstitute.org/igvdata/encode/hg18/broadHistone/SignalK562H3k4me3.tdf"; TDFReader reader = new TDFReader(new ResourceLocator(url)); int version = reader.getVersion(); assertEquals(3, version); assertTrue(reader.compressed); String [] trackNames = reader.getTrackNames(); int nTracks = trackNames.length; assertEquals(1, nTracks); String trackName = trackNames[0]; assertEquals(trackName, "SignalK562H3k4me3.wig.gz"); Set<String> chrNames = reader.getChromosomeNames(); int nChromosomes = chrNames.size(); assertEquals(24, nChromosomes); String datasetName = "/chr1/z0/mean"; TDFDataset dataset = reader.getDataset(datasetName); assertEquals(datasetName, dataset.getName()); TDFTile tile = reader.readTile(dataset, 0); assertNotNull(tile); } }