/** @return a LineIterator that should be closed with CloserUtils */ public static LineIterator openURIForLineIterator(String uri) throws IOException { return new LineIteratorImpl(openURIForLineReader(uri)); }
/** @return a LineIterator that should be closed with CloserUtils */ public static LineIterator openFileForLineIterator(File file) throws IOException { return new LineIteratorImpl(openFileForLineReader(file)); }
/** @return a LineIterator that should be closed with CloserUtils */ public static LineIterator openStreamForLineIterator(final InputStream in) throws IOException { return new LineIteratorImpl(openStreamForLineReader(in)); }
@Override public LineIterator makeSourceFromStream(final InputStream bufferedInputStream) { return new LineIteratorImpl(LineReaderUtil.fromBufferedStream(bufferedInputStream)); }
@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 PAFCodec(String path, Genome genome) { super(PAFFeature.class); this.path = path; this.genome = genome; try { LineIterator reader = new LineIteratorImpl(new AsciiLineReader(ParsingUtils.openInputStream(path))); readActualHeader(reader); } catch (IOException e) { log.error(e.getMessage(), e); } }
public MUTCodec(String path, Genome genome) { super(Mutation.class); this.path = path; this.genome = genome; try { LineIterator reader = new LineIteratorImpl(new AsciiLineReader(ParsingUtils.openInputStream(path))); readActualHeader(reader); } catch (IOException e) { log.error(e.getMessage(), e); } }
header = (VCFHeader) codec.readActualHeader(new LineIteratorImpl(new LineReader() { Iterator<String> iterator = headerLines.iterator();
@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()); } }
@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()); }
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; } }); }
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 }
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; }
/** returns the number of lines in the file that contain a regular expression (decorated with "MV=" and * expected to be in an INFO field in a vcf) * * @param file File to examine * @param regex String containing a regular expression to look for in the file * @return the number of lines that contain regex */ private int grep(final File file, final String regex) { int results = 0; final Pattern pattern = Pattern.compile(".*"+regex+".*"); try (final LineIteratorImpl li = new LineIteratorImpl(new AsciiLineReader(IOUtil.openFileForReading(file)))) { while (li.hasNext()) { final String line = li.next(); if (pattern.matcher(line).matches()) { results++; } } } catch (final IOException e) { e.printStackTrace(); } return results; }
header = (VCFHeader) codec.readActualHeader(new LineIteratorImpl(new LineReader() { Iterator<String> iterator = headerLines.iterator(); @Override
final LineIterator lineIterator = new LineIteratorImpl(LineReaderUtil.fromBufferedStream(bps, LineReaderUtil.LineReaderOption.SYNCHRONOUS)); 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);
final LineIterator lineIterator = new LineIteratorImpl(new SynchronousLineReader(bps)); final VCFCodec headerParser = new VCFCodec(); this.header = (VCFHeader) headerParser.readActualHeader(lineIterator);