@Override public void close() { lineReader.close(); }
@Override public void close() { lineReader.close(); }
@Override public void close() { tabixReader.close(); }
public void close() { lineReader.close(); }
@Override public void close(){ if(this.tabixReader != null){ this.tabixReader.close(); } if(this.bigBedReader != null){ System.err.println("TERE"); this.bigBedReader.close(); } }
@AfterClass public void teardown() throws Exception { tabixReader.close(); }
dbsnpTabixReader.close();
/** Return true if fileName has a valid tabix index. * @throws IOException * */ public static boolean hasTabixIndex(String fileName) throws IOException{ if((new UrlValidator()).isValid(fileName) && fileName.startsWith("ftp")){ // Because of issue #51 return false; } try{ TabixReader tabixReader= new TabixReader(fileName); tabixReader.readLine(); tabixReader.close(); return true; } catch (Exception e){ return false; } }
/** * Test TabixReader.readLine * * @throws java.io.IOException */ @Test public void testTabixReaderReadLine() throws IOException { TabixReader tabixReader = new TabixReader(tabixFile); Assert.assertNotNull(tabixReader.readLine()); tabixReader.close(); } }
System.err.println("tabix -p bed " + fileName + "\n"); } finally { tabixReader.close();