@Override public void close() { for (final InputStream stream : this.streams) { CloserUtil.close(stream); } }
public void close() { for (final InputStream stream : this.streams) { CloserUtil.close(stream); } }
public void close() { for (final InputStream stream : this.streams) { CloserUtil.close(stream); } }
@Override public void close() { if (!closed) { closed = true; CloserUtil.close(it); } }
private void closeCurrent() { if (currentSource != null) { CloserUtil.close(currentSource); } currentSource = null; } @Override
@Override public void close() { for (final InputStream stream : this.streams) { CloserUtil.close(stream); } }
@Override public void close() throws IOException { CloserUtil.close(lineReader); } }
/** * Calls close() on <code>obj</code> if it implements Closeable * * @param obj The potentially closeable object */ public static void close(Object obj) { if (obj != null) { close(Arrays.asList(obj)); } }
/** * Calls close() on <code>obj</code> if it implements Closeable * * @param obj The potentially closeable object */ public static void close(Object obj) { if (obj != null) { close(Arrays.asList(obj)); } }
/** * Closes the underlying stream */ public void close() { if (reader != null) { reader.close(); } for(final InputStream stream : inputs){ CloserUtil.close(stream); } }
/** * Jump so that the next record returned will be the first one from the specified tile. */ public void seekToTile(final int oneBasedTileNumber) { CloserUtil.close(parser); currentTile = oneBasedTileNumber; initializeParser(); }
void assertProperFileStructure(final File file, final int numClusters, final InputStream stream) { final long elementsInFile = file.length() - HEADER_SIZE; if (numClusters != elementsInFile) { CloserUtil.close(stream); throw new PicardException("Expected " + numClusters + " in file " + file.getAbsolutePath() + " but found " + elementsInFile); } }
private static Map<String, File> createOutputMapFromFile(final File outputMapFile) { final Map<String, File> outputMap = new HashMap<>(); final TabbedTextFileWithHeaderParser parser = new TabbedTextFileWithHeaderParser(outputMapFile); for (final TabbedTextFileWithHeaderParser.Row row : parser) { final String id = row.getField("READ_GROUP_ID"); final String output = row.getField("OUTPUT"); final File outputPath = new File(output); outputMap.put(id, outputPath); } CloserUtil.close(parser); return outputMap; }
private static Map<String, File> createOutputMapFromFile(final File outputMapFile) { final Map<String, File> outputMap = new HashMap<>(); final TabbedTextFileWithHeaderParser parser = new TabbedTextFileWithHeaderParser(outputMapFile); for (final TabbedTextFileWithHeaderParser.Row row : parser) { final String id = row.getField("READ_GROUP_ID"); final String output = row.getField("OUTPUT"); final File outputPath = new File(output); outputMap.put(id, outputPath); } CloserUtil.close(parser); return outputMap; }
void writeDesignFastaFile(final File file, final IntervalList baits) { final BufferedWriter out = IOUtil.openFileForBufferedWriting(file); for (final Interval i : baits) { writeBaitFasta(out, i, false); } CloserUtil.close(out); }
public void close() { SAMReaders readers = resourcePool.getAvailableReaders(); for(SAMReaderID readerID: readerIDs) { SamReader reader = readers.getReader(readerID); CloserUtil.close(reader); } }
private void write(File output) throws IOException { log.info("Writing simplified variant calls to " + output.getName() + ". Only use this output if your pipeline is unable to process variants in VCF breakend notation."); File working = FileSystemContext.getWorkingFileFor(output); VariantContextWriter vcfWriter = processContext.getVariantContextWriter(working, true); Collections.sort(outputBuffer, IdsvVariantContext.ByLocationStart); for (IdsvVariantContext v : outputBuffer) { vcfWriter.add(v); } CloserUtil.close(vcfWriter); FileHelper.move(working, output, true); } private void load(File breakendCalls) {
/** * Convenience method to read all the Metric beans from a metrics file. * @param file to be read. * @return list of beans from the file. */ public static <T extends MetricBase> List<T> readBeans(final File file) { final MetricsFile<T, ?> metricsFile = new MetricsFile<>(); final Reader in = IOUtil.openFileForBufferedReading(file); metricsFile.read(in); CloserUtil.close(in); return metricsFile.getMetrics(); }
/** * Convenience method to read all the Metric beans from a metrics file. * @param file to be read. * @return list of beans from the file. */ public static <T extends MetricBase> List<T> readBeans(final File file) { final MetricsFile<T, ?> metricsFile = new MetricsFile<>(); final Reader in = IOUtil.openFileForBufferedReading(file); metricsFile.read(in); CloserUtil.close(in); return metricsFile.getMetrics(); }
private int countReads(File samFile) { SamReader reader = SamReaderFactory.makeDefault().open(samFile); int count = 0; for (Iterator it = reader.iterator(); it.hasNext(); ) { it.next(); count++; } CloserUtil.close(reader); return count; } }