public void close() { if(currentIterator != null) { currentIterator.close(); } }
/** * Close down all open iterators. */ @Override public void close() { // Iterators not in the priority queue have already been closed; only close down the iterators that are still in the priority queue. for (CloseableIterator<SAMRecord> iterator : pq) iterator.close(); }
@Override public void close() { if (iterator instanceof CloseableIterator) { ((CloseableIterator) this.iterator).close(); } }
void close() { if (iterator != null) { iterator.close(); iterator = null; } } }
/** * {@inheritDoc} */ public void close() { iterator.close(); }
@Override public void close() { if (iterator instanceof CloseableIterator) { ((CloseableIterator) this.iterator).close(); } }
public void close() { for (CloseableIterator<Alignment> iter : allIterators) { iter.close(); } allIterators.clear(); iteratorQueue.clear(); }
public void close() { if (it != null) it.close(); if (reader != null) reader.close(); }
public void onTraversalDone(Integer sum) { if ( dbsnpIterator != null ) dbsnpIterator.close(); vcfwriter.close(); } }
/** Consumes the contents of the iterator and returns it as a List. */ default List<T> toList() { final List<T> list = new ArrayList<>(); while (hasNext()) list.add(next()); close(); return list; }
private void advanceTile() { if(nextTile == null){ throw new NoSuchElementException("No more tiles to advance!"); } if(currentIterator != null) { currentIterator.close(); } currentIterator = makeTileIterator(tileToFiles.get(nextTile)); currentTile = nextTile; nextTile = tileToFiles.higherKey(nextTile); }
public void seekToTile(int oneBasedTileNumber) { nextTile = oneBasedTileNumber; if(!tileToFiles.containsKey(oneBasedTileNumber)) { throw new PicardException("PerTileParser does not contain key(" + oneBasedTileNumber +") keys available (" + StringUtil.join(",", new ArrayList<Integer>(tileToFiles.keySet())) + ")"); } if(currentIterator != null) { currentIterator.close(); } currentIterator = null; }
public static void main(String[] args) throws IOException { AlignmentReader reader = AlignmentReaderFactory.getReader(args[0], false); CloseableIterator<Alignment> iter = reader.iterator(); PairedEndStats stats = compute(iter, .1, 99.9); iter.close(); reader.close(); System.out.println(args[0] + "\t" + stats.averageInsertSize + "\t" + stats.medianInsertSize + "\t" + stats.stddevInsertSize + "\t" + stats.madInsertSize); }
private <E> void consumeAll(final Collection<E> collection, final CloseableIterator<E> iterator) { while (iterator.hasNext()) { collection.add(iterator.next()); } iterator.close(); }
public void vcfTester(String inVcf){ // Credit: https://www.biostars.org/p/262943/ VCFFileReader r=new VCFFileReader(new File(inVcf)); CloseableIterator<VariantContext> t=r.iterator(); while(t.hasNext()){ t.next(); } t.close(); r.close(); }
static Queue<String> loadContigPositions(final File inputFile) { final VCFFileReader reader = new VCFFileReader(inputFile, false); final Queue<String> contigPositions = new LinkedList<String>(); final CloseableIterator<VariantContext> iterator = reader.iterator(); while (iterator.hasNext()) contigPositions.add(getContigPosition(iterator.next())); iterator.close(); reader.close(); return contigPositions; }
@Test public void testUnmapped() { final String alignmentFromKris = "0\t4\t*\t0\t0\t*\t*\t0\t0\tGCCTCGTAGTGCGCCATCAGTCTATCGATGTCGTTG\t44\"44===;;;;;;;;;::::88844\"4\"\"\"\"\"\"\"\"\n"; final SamReader samReader = createSamFileReader(alignmentFromKris); final CloseableIterator<SAMRecord> iterator = samReader.iterator(); while (iterator.hasNext()) { iterator.next(); } iterator.close(); CloserUtil.close(samReader); }
@Test public void testIterator() throws Exception { String entriesFile = TestUtils.DATA_DIR + "goby/GDFQPGI-pickrellNA18486_yale.entries"; GobyAlignmentQueryReader reader = new GobyAlignmentQueryReader(entriesFile); CloseableIterator<Alignment> iter = reader.iterator(); assertTrue(iter.hasNext()); iter.close(); reader.close(); }
private void checkNumber(String chr, int start, int end, int expected_count) throws IOException { CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, false); int counted = 0; while (iter.hasNext()) { Alignment a = iter.next(); counted++; assertNotNull(a); } iter.close(); assertEquals(expected_count, counted); }
public void timeExtractTag(int reps) throws IOException { for(int i = 0; i < reps; i++) { final SamReader reader = SamReaderFactory.makeDefault().open(inputFile); CloseableIterator<SAMRecord> iterator = reader.iterator(); while(iterator.hasNext()) { SAMRecord read = iterator.next(); read.getAttribute("OQ"); } iterator.close(); reader.close(); } }