Class CramRecordReader

    • Field Detail

      • APDelta

        protected final boolean APDelta
    • Constructor Detail

      • CramRecordReader

        public CramRecordReader​(BitInputStream coreInputStream,
                                Map<Integer,​ByteArrayInputStream> externalInputMap,
                                CompressionHeader header,
                                int refId,
                                ValidationStringency validationStringency)
        Initialize a Cram Record Reader
        Parameters:
        coreInputStream - Core data block bit stream, to be read by non-external Encodings
        externalInputMap - External data block byte stream map, to be read by external Encodings
        header - the associated Cram Compression Header
        refId - the reference sequence ID to assign to these records
        validationStringency - how strict to be when reading this CRAM record
    • Method Detail

      • read

        public void read​(CramCompressionRecord cramRecord)
        Read a Cram Compression Record, using this class's Encodings
        Parameters:
        cramRecord - the Cram Compression Record to read into