@Override public boolean hasNext() { try { return reader.hasNext(); } catch (final NullPointerException npe) { return false; } } }
/** * {@inheritDoc} */ public boolean hasNext() { return iterator.hasNext(); }
Alignment advance() { Alignment tmp = nextRecord; nextRecord = (iterator.hasNext() ? iterator.next() : null); return tmp; }
public boolean hasNext() { try { return this.it.hasNext(); } catch ( RuntimeException e ) { // we need to catch RuntimeExceptions here because the Picard code is throwing them (among SAMFormatExceptions) sometimes throw new UserException.MalformedBAM(source, e.getMessage()); } }
/** 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; }
public void maybeAdvance() { if(!hasNext()) { throw new NoSuchElementException(); } if(currentIterator == null || !currentIterator.hasNext()) { advanceTile(); } }
public void maybeAdvance() { if(!hasNext()) { throw new NoSuchElementException(); } if(currentIterator == null || !currentIterator.hasNext()) { advanceTile(); } }
public int count(CloseableIterator<PicardAlignment> iter) { int counter = 0; while (iter.hasNext()) { iter.next(); counter++; } return counter; }
public int count(CloseableIterator<PicardAlignment> iter) { int counter = 0; while (iter.hasNext()) { iter.next(); counter++; } return counter; }
public static void main(String[] args) throws IOException { Globals.setHeadless(true); CGIAlignmentReader reader = new CGIAlignmentReader("http://philtest.batcave.net/query.cgi?file=input.sam"); String chr = "gi|66043271|ref|NC_007005.1|"; int start = 800; int end = 900; CloseableIterator<PicardAlignment> iter = reader.query(chr, start, end, false); while (iter.hasNext()) { Alignment a = iter.next(); System.out.println(a); } }
@Override public boolean nextKeyValue() { if (!iterator.hasNext()) { reachedEnd = true; return false; } final SAMRecord r = iterator.next(); key.set(getKey(r)); record.set(r); return true; } }
private int countElements(final CloseableIterator<SAMRecord> it) { int num; for (num = 0; it.hasNext(); ++num, it.next()) { } it.close(); return num; }
@Test public void test_chrM_1500_location() throws IOException { CRAMFileReader reader = new CRAMFileReader(cramFile, indexFile, source); reader.setValidationStringency(ValidationStringency.SILENT); CloseableIterator<SAMRecord> iterator = reader.queryAlignmentStart("chrM", 1500); Assert.assertTrue(iterator.hasNext()); SAMRecord record = iterator.next(); Assert.assertEquals(record.getReferenceName(), "chrM"); Assert.assertTrue(record.getAlignmentStart() >= 1500); }
private AlignmentInterval getAlignmentInterval() throws Exception { ResourceLocator rl = new ResourceLocator(path); AlignmentReader samReader = AlignmentReaderFactory.getReader(rl); CloseableIterator<Alignment> iter = samReader.query(chr, start, end, contained); List<Alignment> list = new ArrayList<Alignment>(); while(iter.hasNext()){ list.add(iter.next()); } AlignmentInterval interval = new AlignmentInterval(chr, start, end, list, null, null, null); return interval; }
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 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(); }
@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); }
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(); } }