private static void dumpTileData(TDFReader reader, String chrName, TDFTile tile, PrintStream ps) { int nTracks = reader.getTrackNames().length; int nBins = tile.getSize(); if (nBins > 0) { for (int b = 0; b < nBins; b++) { ps.print(chrName); ps.print("\t" + tile.getStartPosition(b)); ps.print("\t" + tile.getEndPosition(b)); for (int t = 0; t < nTracks; t++) { ps.print("\t" + tile.getValue(t, b)); } ps.println(); } } }
String[] trackNames = reader.getTrackNames(); for (String trackName : trackNames) { System.out.println(trackName);
System.out.println("Null tile: " + dsName + " [" + tileNumber + "]"); } else { int nTracks = reader.getTrackNames().length; int nBins = tile.getSize(); if (nBins > 0) {
int nTracks = reader.getTrackNames().length; if(nTracks > 1){ throw new RuntimeException("More than one track found in tdf file " + ibfFile);
@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); } }
boolean multiTrack = reader.getTrackNames().length > 1; for (String heading : reader.getTrackNames()) {
int nTracks = this.getTrackNames().length; // TODO -- is there a more direct way to know this? double binSize = (genome.getNominalLength() / 1000) / binCount; Accumulator[][] accumulators = new Accumulator[nTracks][binCount];
/** * Test of createDataset method, of class IBFWriter. */ @Test public void testCreateFile() { File testFile = new File("test2.tdf"); testFile.deleteOnExit(); TDFWriter writer = new TDFWriter(testFile, "hg18", type, trackLine, trackNames, wfs, false); writer.closeFile(); TDFReader reader = TDFReader.getReader(testFile.getAbsolutePath()); String[] tn = reader.getTrackNames(); assertEquals(trackNames.length, tn.length); for (int i = 0; i < tn.length; i++) { assertEquals(trackNames[i], tn[i]); } assertEquals(type, reader.getTrackType()); assertEquals(trackLine, reader.getTrackLine()); reader.close(); }