public Alignment readElem() { Alignment alignment = null; SAMRecord record = null; if(iterator.hasNext()){ record = iterator.next(); alignment = AlignmentConverter.buildAlignment(record); } return alignment; }
public SAMRecord read() { while(iterator.hasNext()) { SAMRecord record = iterator.next(); if (filter != 0 && (record.getFlags() & filter) != 0) { continue; } return record; } return null; }
private void readAllAlignments(final SamReaderFactory readerFactory) { SamReader fromExternalProgram = readerFactory.open(SamInputResource.of(aligner.getInputStream())); SAMRecordIterator it = fromExternalProgram.iterator(); while (it.hasNext()) { SAMRecord r = it.next(); buffer.add(r); outstandingReads.decrementAndGet(); } log.info(String.format("Reader thread complete. %s reads in output buffer", buffer.size())); } /**
@Test(description = "This test checks that records validation is deferred until they are retrieved") public void noValidationFailureOnContainerOpen() { try (SAMRecordIterator cramIteratorOverInvalidRecords = getCramFileIterator(ValidationStringency.STRICT)) { Assert.assertTrue(cramIteratorOverInvalidRecords.hasNext()); } }
public void process() throws IOException { timer = Stopwatch.createStarted(); openFile(); while (iterator.hasNext()) { processRecord(iterator.next()); } dumpStats(); }
public void process() throws IOException { timer = Stopwatch.createStarted(); openFile(); while (iterator.hasNext()) { processRecord(iterator.next()); } dumpStats(); }
@Test(dataProvider = "sortsFailCramWithoutIndex", expectedExceptions = IllegalStateException.class) public void testCramSortFail(String file, String fileReference, SAMFileHeader.SortOrder order) throws Exception { final CRAMFileReader cramFileReader = getCramFileReader(file, fileReference); final SAMRecordIterator samRecordIterator = cramFileReader.getIterator().assertSorted(order); Assert.assertTrue(samRecordIterator.hasNext()); while (samRecordIterator.hasNext()) { Assert.assertNotNull(samRecordIterator.next()); } }
@Override public boolean nextKeyValue() { if (!iterator.hasNext()) return false; final SAMRecord r = iterator.next(); key.set(BAMRecordReader.getKey(r)); record.set(r); return true; } }
@Override public boolean nextKeyValue() { if (!iterator.hasNext()) return false; final SAMRecord r = iterator.next(); key.set(BAMRecordReader.getKey(r)); record.set(r); return true; } }
@Test(dataProvider = "sortsCramWithoutIndex") public void testCramSort(String file, String fileReference, SAMFileHeader.SortOrder order) throws Exception { final CRAMFileReader cramFileReader = getCramFileReader(file, fileReference); final SAMRecordIterator samRecordIterator = cramFileReader.getIterator().assertSorted(order); Assert.assertTrue(samRecordIterator.hasNext()); while (samRecordIterator.hasNext()) { Assert.assertNotNull(samRecordIterator.next()); } }
@Override public boolean nextKeyValue() { if (!iterator.hasNext()) return false; final SAMRecord r = iterator.next(); key.set(BAMRecordReader.getKey(r)); record.set(r); return true; } }
@Test(expectedExceptions = SAMException.class) public void throwOnRecordValidationFailure() { try (SAMRecordIterator cramIteratorOverInvalidRecords = getCramFileIterator(ValidationStringency.STRICT)) { while (cramIteratorOverInvalidRecords.hasNext()) { cramIteratorOverInvalidRecords.next(); } } }
@Test(expectedExceptions = CRAMException.class) public void testExceptionWhileReadingWithWrongReference() throws IOException { final CramTestCase test = new CramTestCase(); // try reading the CRAM file with the incorrect ref source that does not upper case bases: final CRAMFileReader reader = new CRAMFileReader(new ByteArrayInputStream(test.cramData), (File) null, test.referenceSourceMixedCase, ValidationStringency.STRICT); final SAMRecordIterator iterator = reader.getIterator(); // expect an exception here due to slice MD5 mismatch: iterator.hasNext(); }
private int countRecords(final SamReader reader) { int count = 0; try (final SAMRecordIterator iter = reader.iterator()) { while (iter.hasNext()) { iter.next(); count++; } } return count; }
@Test(expectedExceptions = IllegalStateException.class) public void testSortsDisagree() throws Exception { SAMRecordIterator it = SamReaderFactory.makeDefault().open(new File(COORDINATE_SORTED_FILE)).iterator(); try { it.assertSorted(SAMFileHeader.SortOrder.queryname); while (it.hasNext()) { it.next(); } Assert.fail("Queryname assertion should have failed on coordinate sorted file but didn't"); } finally { it.close(); } }
private int countRecordsInQueryInterval(final SamReader reader, final QueryInterval query) { final SAMRecordIterator iter = reader.queryOverlapping(new QueryInterval[]{query}); int count = 0; while (iter.hasNext()) { iter.next(); count++; } iter.close(); return count; }
@Test(dataProvider = "validSorts") public void testSortAssertionValid(String file, SAMFileHeader.SortOrder order) { SAMRecordIterator it = SamReaderFactory.makeDefault().open(new File(file)).iterator(); try { it.assertSorted(order); while (it.hasNext()) { it.next(); } } finally { it.close(); } }
@Test(dataProvider = "invalidSorts", expectedExceptions = IllegalStateException.class) public void testSortAssertionFails(String file, SAMFileHeader.SortOrder order) throws Exception { SAMRecordIterator it = SamReaderFactory.makeDefault().open(new File(file)).iterator(); try { it.assertSorted(order); while (it.hasNext()) { it.next(); } Assert.fail("Iterated successfully over " + file + " with invalid sort assertion: " + order.name()); } finally { it.close(); } }
private void validateUq(final File input, final File reference) { final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(reference).open(input); final SAMRecordIterator iterator = reader.iterator(); while (iterator.hasNext()){ SAMRecord rec = iterator.next(); if (!rec.getReadUnmappedFlag()) Assert.assertNotNull(rec.getAttribute("UQ")); } }