@Override public Set<String> getReferenceNames() { Set<String> result = new HashSet<String>(); for (String key: tdf.getDatasetNames()) { int rawPos = key.indexOf("/raw"); if (rawPos > 1) { // Keys will have the form "/chr1/raw". result.add(key.substring(1, rawPos)); } } return result; }
public static void dumpDatasets(String ibfFile) { TDFReader reader = TDFReader.getReader(ibfFile); System.out.println("DATASETS"); for (String dsName : reader.getDatasetNames()) { System.out.println(dsName); TDFDataset ds = reader.getDataset(dsName); System.out.println("Attributes"); for (Map.Entry<String, String> entry : ds.attributes.entrySet()) { System.out.println("\t" + entry.getKey() + " = " + entry.getValue()); } System.out.println(); System.out.println("Tile Positions"); for (int i = 0; i < ds.nTiles; i++) { System.out.print("\t" + ds.tilePositions[i]); } System.out.println(); } }
public static void dumpAllTiles(String ibfFile) { TDFReader reader = TDFReader.getReader(ibfFile); System.out.println("DATASETS"); for (String dsName : reader.getDatasetNames()) { System.out.println(dsName); TDFDataset ds = reader.getDataset(dsName); for (int i = 0; i < ds.nTiles; i++) { TDFTile tile = ds.getTile(i); if (tile != null) { System.out.println("Tile: " + i); dumpTileData(reader, "", tile, System.out); } } } }
public static void tdfToBedgraph(String tdfFile, String bedGraphFile) throws FileNotFoundException { TDFReader reader = null; PrintStream ps = null; try { reader = TDFReader.getReader(tdfFile); ps = new PrintStream(new BufferedOutputStream(new FileOutputStream(bedGraphFile))); String trackLine = reader.getTrackLine(); if (trackLine != null && trackLine.length() > 0) { ps.println(trackLine); } for (String dsName : reader.getDatasetNames()) { String[] tokens = dsName.split("/"); String chrName = tokens[1]; if (!chrName.equals(Globals.CHR_ALL) && dsName.contains("raw")) { TDFDataset ds = reader.getDataset(dsName); for (int i = 0; i < ds.nTiles; i++) { TDFTile tile = ds.getTile(i); if (tile != null) { dumpTileData(reader, chrName, tile, ps); } } } } } finally { if (reader != null) reader.close(); if (ps != null) ps.close(); } }
for (String dsName : reader.getDatasetNames()) { System.out.println(dsName); TDFDataset ds = reader.getDataset(dsName);
private void tstCountBamList(String listArg) throws Exception { String outputFile = TestUtils.TMP_OUTPUT_DIR + "file_"; String[] opts = new String[]{"--strands=read", "--strands=first", ""}; for (int ind = 0; ind < opts.length; ind++) { String opt = opts[ind]; String fullout = outputFile + ind + ".tdf"; String input = "count " + opt + " " + listArg + " " + fullout + " " + hg18id; String[] args = input.split("\\s+"); igvTools.run(args); TDFReader reader = TDFReader.getReader(fullout); assertTrue(reader.getDatasetNames().size() > 0); } }
Collection<String> dsNames = tdf.getDatasetNames(); for (String dsName: dsNames) {
for (String dsName : reader.getDatasetNames()) {
assertTrue(reader.getDatasetNames().size() > 0); if (query) { for (String name : reader.getDatasetNames()) { TDFDataset ds = reader.getDataset(name); List<TDFTile> tiles = ds.getTiles();