/** * Initialize a Cram Record Reader from a Slice * * @param header the associated Cram Compression Header * @param validationStringency how strict to be when reading this CRAM record */ public CramRecordReader createCramRecordReader(final CompressionHeader header, final ValidationStringency validationStringency) { return new CramRecordReader(getCoreBlockInputStream(), getExternalBlockInputMap(), header, sequenceId, validationStringency); }
/** * Initialize a Cram Record Reader from a Slice * * @param header the associated Cram Compression Header * @param validationStringency how strict to be when reading this CRAM record */ public CramRecordReader createCramRecordReader(final CompressionHeader header, final ValidationStringency validationStringency) { return new CramRecordReader(getCoreBlockInputStream(), getExternalBlockInputMap(), header, sequenceId, validationStringency); }
final CramRecordReader reader = new CramRecordReader(ValidationStringency.SILENT); dataReaderFactory.buildReader(reader, new DefaultBitInputStream(new ByteArrayInputStream( slice.coreBlock.getRawContent())), inputMap, c.header, slice.sequenceId);
private CramCompressionRecord read(final byte[] dataBytes, final CompressionHeader header, final int refId, final Map<Integer, ByteArrayInputStream> inputMap) throws IOException { try (final ByteArrayInputStream is = new ByteArrayInputStream(dataBytes); final BitInputStream bis = new DefaultBitInputStream(is)) { final CramRecordReader reader = new CramRecordReader(bis, inputMap, header, refId, ValidationStringency.DEFAULT_STRINGENCY); final CramCompressionRecord recordToRead = new CramCompressionRecord(); reader.read(recordToRead); return recordToRead; } }