public static LineReader openStreamForLineReader(final InputStream in) throws IOException { return new SynchronousLineReader(in); }
public static LineReader openStdinForLineReader() throws IOException { return new SynchronousLineReader(System.in); }
@Override public LineIterator makeSourceFromStream(final InputStream bufferedInputStream) { return new LineIteratorImpl(new SynchronousLineReader(bufferedInputStream)); }
@Override public LineIterator makeSourceFromStream(final InputStream bufferedInputStream) { return new LineIteratorImpl(new SynchronousLineReader(bufferedInputStream)); }
public static LineReader openURIForLineReader(String uri) throws IOException { return new SynchronousLineReader(openURIForReading(uri)); } /** @return a LineIterator that should be closed with CloserUtils */
public static LineReader openFileForLineReader(File file) throws IOException { return new SynchronousLineReader(openFileForReading(file)); } /** @return a LineIterator that should be closed with CloserUtils */
public static VariantContextContainer readAllVCs(final File input, final VCFCodec codec) throws FileNotFoundException { final LineIterator lineIterator = new LineIteratorImpl(new SynchronousLineReader(new BufferedInputStream(new FileInputStream(input)))); final VCFHeader vcfHeader = (VCFHeader) codec.readActualHeader(lineIterator); return new VariantContextTestProvider.VariantContextContainer(vcfHeader, new VariantContextTestProvider.VCIterable<LineIterator>(codec, vcfHeader) { @Override public boolean hasNext() { return lineIterator.hasNext(); } @Override public LineIterator nextSource() { return lineIterator; } }); }
@Test public void testLineReaderIterator_readerConstructor() throws Exception { final File filePath = new File(TestUtils.DATA_DIR + "gwas/smallp.gwas"); final LineIterator lineIterator = new LineIteratorImpl(new SynchronousLineReader(new InputStreamReader(new PositionalBufferedStream(new FileInputStream(filePath))))); final BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(filePath))); while (lineIterator.hasNext()) { Assert.assertEquals(lineIterator.next(), br.readLine()); } Assert.assertNull(br.readLine()); } }
public LineIterator getLineIterator() { try { return new LineIteratorImpl(new SynchronousLineReader(new PositionalBufferedStream(new FileInputStream(hapMapFile)))); } catch (FileNotFoundException e) { Assert.fail("Unable to open hapmap file : " + hapMapFile); } return null; // for intellij, it doesn't know that assert.fail is fatal }
@Test public void testLineReaderIterator_streamConstructor() throws Exception { final File filePath = new File(TestUtils.DATA_DIR + "gwas/smallp.gwas"); final LineIterator lineIterator = new LineIteratorImpl(new SynchronousLineReader(new PositionalBufferedStream(new FileInputStream(filePath)))); final BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(filePath))); while (lineIterator.hasNext()) { Assert.assertEquals(lineIterator.next(), br.readLine()); } Assert.assertNull(br.readLine()); }
private VCFHeader createHeader(String headerStr) { VCFCodec codec = new VCFCodec(); VCFHeader header = (VCFHeader) codec.readActualHeader(new LineIteratorImpl(new SynchronousLineReader( new StringReader(headerStr)))); Assert.assertEquals(header.getMetaDataInInputOrder().size(), VCF4headerStringCount); return header; }
@Override public Iterator<T> iterator() { return this; } }
@Override public Iterator<T> iterator() { return this; } }
final LineIterator lineIterator = new LineIteratorImpl(new SynchronousLineReader(bps)); final VCFCodec headerParser = new VCFCodec(); this.header = (VCFHeader) headerParser.readActualHeader(lineIterator);
final LineIterator lineIterator = new LineIteratorImpl(new SynchronousLineReader(bps)); final VCFCodec headerParser = new VCFCodec(); this.header = (VCFHeader) headerParser.readActualHeader(lineIterator);