@Override public void close() { tdf.close(); }
public static void dumpIndex(String tdfFile) { TDFReader reader = TDFReader.getReader(tdfFile); reader.dumpIndex(); reader.close();; }
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(); } }
reader.close(); return screenWiggleLocusInfoList;
/** * Test of createGroup method, of class IBFWriter. */ @Test public void testCreateGroup() { File testFile = new File("test1.tdf"); testFile.deleteOnExit(); String groupName = "/chr1"; TDFWriter writer = new TDFWriter(testFile, "hg18", type, trackLine, trackNames, wfs, false); TDFGroup group = writer.createGroup(groupName); group.setAttribute("attKey", "attValue"); group.setAttribute("attKey2", "attValue2"); writer.closeFile(); TDFReader reader = TDFReader.getReader(testFile.getAbsolutePath()); group = reader.getGroup(groupName); assertEquals(groupName, group.getName()); assertEquals(2, group.attributes.size()); assertEquals("attValue", group.attributes.get("attKey")); assertEquals("attValue2", group.attributes.get("attKey2")); reader.close(); }
/** * 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(); }
reader.close();