Class ReadTag

  • All Implemented Interfaces:
    Comparable<ReadTag>

    public class ReadTag
    extends Object
    implements Comparable<ReadTag>
    CRAM counterpart of SAMTag. TODO: consider merging/dropping this class in favour of SAMTag or a SAMTag implementation.
    • Field Detail

      • keyType3Bytes

        public String keyType3Bytes
      • keyType3BytesAsInt

        public int keyType3BytesAsInt
    • Constructor Detail

      • ReadTag

        public ReadTag​(int id,
                       byte[] dataAsByteArray,
                       ValidationStringency validationStringency)
    • Method Detail

      • name3BytesToInt

        public static int name3BytesToInt​(byte[] name)
      • nameType3BytesToInt

        public static int nameType3BytesToInt​(String name,
                                              char type)
      • intToNameType3Bytes

        public static String intToNameType3Bytes​(int value)
      • intToNameType4Bytes

        public static String intToNameType4Bytes​(int value)
      • deriveTypeFromKeyAndType

        public static ReadTag deriveTypeFromKeyAndType​(String keyAndType,
                                                       Object value)
      • deriveTypeFromValue

        public static ReadTag deriveTypeFromValue​(String key,
                                                  Object value)
      • getKey

        public String getKey()
      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class Object
      • getValue

        public Object getValue()
      • getKeyAndType

        public String getKeyAndType()
      • getValueAsByteArray

        public byte[] getValueAsByteArray()
      • setIndex

        public void setIndex​(byte i)
      • getIndex

        public byte getIndex()
      • writeSingleValue

        public static byte[] writeSingleValue​(byte tagType,
                                              Object value,
                                              boolean isUnsignedArray)