String json = aceptaDefault(); JSONParser parser = new JSONParser(); ContainerFactory orderedKeyFactory = new ContainerFactory() { public List createArrayContainer() { return new LinkedList(); } public Map createObjectContainer() { return new LinkedHashMap(); } }; Object obj = parser.parse(json,orderedKeyFactory); LinkedHashMap map = (LinkedHashMap)obj;
/** * Write a CRAM file header and SAM header to the stream. * @param header SAMFileHeader to write */ public void writeHeader(final SAMFileHeader header) { // TODO: header must be written exactly once per writer life cycle. offset = CramIO.writeHeader(cramVersion, outputStream, header, cramID); }
List<CramCompressionRecord> getRecords(final Slice slice, final CompressionHeader header, final ValidationStringency validationStringency) throws IllegalArgumentException, IllegalAccessException { return getRecords(null, slice, header, validationStringency); } }
@Test public void testMultiref() { final ContainerFactory factory = new ContainerFactory(getSAMFileHeaderForTests(), 10); final Container container = factory.buildContainer(getMultiRefRecords()); assertContainerState(container, 10, Slice.MULTI_REFERENCE, Slice.NO_ALIGNMENT_START, Slice.NO_ALIGNMENT_SPAN); }
@Test public void testMapped() { final int recordCount = 10; final int sequenceId = 0; final int alignmentStart = 1; final int alignmentSpan = 12; final ContainerFactory factory = new ContainerFactory(getSAMFileHeaderForTests(), 10); final Container container = factory.buildContainer(getSingleRefRecords(recordCount)); assertContainerState(container, recordCount, sequenceId, alignmentStart, alignmentSpan); }
@Test public void testUnmappedNoAlignmentStart() { final ContainerFactory factory = new ContainerFactory(getSAMFileHeaderForTests(), 10); final Container container = factory.buildContainer(getUnmappedNoStartRecords()); assertContainerState(container, 10, SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, Slice.NO_ALIGNMENT_START, Slice.NO_ALIGNMENT_SPAN); }
@Test public void testUnmappedNoReferenceId() { final ContainerFactory factory = new ContainerFactory(getSAMFileHeaderForTests(), 10); final Container container = factory.buildContainer(getUnmappedNoRefRecords()); assertContainerState(container, 10, SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX, Slice.NO_ALIGNMENT_START, Slice.NO_ALIGNMENT_SPAN); }
public static void restoreQualityScores(final byte defaultQualityScore, final List<CramCompressionRecord> records) { for (final CramCompressionRecord record : records) restoreQualityScores(defaultQualityScore, record); }
@Override protected CramHeader readHeader(InputStream is) throws IOException { try { return CramIO.readCramHeader(is); } catch (IOException e) { throw e; } catch (Exception ee) { return null; } } };
@Override public boolean hasNext() { if (eof) return false; if (nextContainer == null) readNextContainer(); return !eof; }
@Override public Container next() { return currentBoundary.next(); }
public static CramSpanContainerIterator fromFileSpan(final SeekableStream seekableStream, final long[] coordinates) throws IOException { return new CramSpanContainerIterator(seekableStream, coordinates); }
private OutputStream prepareCRAMStream( OutputStream out, final SAMFormat format, final SAMFileHeader header) throws IOException { CramIO.writeHeader(CramVersions.DEFAULT_CRAM_VERSION, out, header, null); return out; }
public static void restoreQualityScores(final byte defaultQualityScore, final List<CramCompressionRecord> records) { for (final CramCompressionRecord record : records) restoreQualityScores(defaultQualityScore, record); }
@Override public boolean hasNext() { if (eof) return false; if (nextContainer == null) readNextContainer(); return !eof; }
private OutputStream prepareCRAMStream( OutputStream out, final SAMFormat format, final SAMFileHeader header) throws IOException { CramIO.writeHeader(CramVersions.DEFAULT_CRAM_VERSION, out, header, null); return out; }
public static void restoreQualityScores(final byte defaultQualityScore, final List<CramCompressionRecord> records) { for (final CramCompressionRecord record : records) restoreQualityScores(defaultQualityScore, record); }
/** * Write a CRAM file header and SAM header to the stream. * @param header SAMFileHeader to write */ public void writeHeader(final SAMFileHeader header) { // TODO: header must be written exactly once per writer life cycle. offset = CramIO.writeHeader(cramVersion, outputStream, header, cramID); }
private OutputStream prepareCRAMStream( OutputStream out, final SAMFormat format, final SAMFileHeader header) throws IOException { CramIO.writeHeader(CramVersions.DEFAULT_CRAM_VERSION, out, header, null); return out; }
/** * Write a CRAM file header and SAM header to the stream. * * @param header * SAMFileHeader to write */ public void writeHeader(final SAMFileHeader header) { // TODO: header must be written exactly once per writer life cycle. offset = CramIO.writeHeader(cramVersion, outputStream, header, cramID); }