htsjdk.samtools.cram.structure
Class ReadTag

java.lang.Object
  htsjdk.samtools.cram.structure.ReadTag

All Implemented Interfaces:

java.lang.Comparable<ReadTag>

public class ReadTag
extends java.lang.Object
implements java.lang.Comparable<ReadTag>

Field Summary

static int	BQZ
short	code
java.lang.String	keyType3Bytes
int	keyType3BytesAsInt
static int	OQZ

Constructor Summary

ReadTag(int id, byte[] dataAsByteArray)

ReadTag(java.lang.String key, char type, java.lang.Object value)

Method Summary

int	compareTo(ReadTag o)
SAMRecord.SAMTagAndValue	createSAMTag()
static ReadTag	deriveTypeFromKeyAndType(java.lang.String keyAndType, java.lang.Object value)
static ReadTag	deriveTypeFromValue(java.lang.String key, java.lang.Object value)
boolean	equals(java.lang.Object obj)
byte	getIndex()
java.lang.String	getKey()
java.lang.String	getKeyAndType()
static char	getTagValueType(java.lang.Object value)
char	getType()
java.lang.Object	getValue()
byte[]	getValueAsByteArray()
int	hashCode()
static java.lang.String	intToNameType3Bytes(int value)
static java.lang.String	intToNameType4Bytes(int value)
static void	main(java.lang.String[] args)
static int	name3BytesToInt(byte[] name)
static int	nameType3BytesToInt(java.lang.String name, char type)
static java.lang.Object	readSingleValue(byte tagType, java.nio.ByteBuffer byteBuffer, ValidationStringency validationStringency)
static java.lang.Object	restoreValueFromByteArray(char type, byte[] array)
void	setIndex(byte i)
static byte[]	writeSingleValue(byte tagType, java.lang.Object value, boolean isUnsignedArray)

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Field Detail

OQZ

public static final int OQZ

See Also:

Constant Field Values

BQZ

public static final int BQZ

See Also:

Constant Field Values

keyType3Bytes

public java.lang.String keyType3Bytes

keyType3BytesAsInt

public int keyType3BytesAsInt

code

public short code

Constructor Detail

ReadTag

public ReadTag(int id,
               byte[] dataAsByteArray)

ReadTag

public ReadTag(java.lang.String key,
               char type,
               java.lang.Object value)

Method Detail

name3BytesToInt

public static int name3BytesToInt(byte[] name)

nameType3BytesToInt

public static int nameType3BytesToInt(java.lang.String name,
                                      char type)

intToNameType3Bytes

public static java.lang.String intToNameType3Bytes(int value)

intToNameType4Bytes

public static java.lang.String intToNameType4Bytes(int value)

createSAMTag

public SAMRecord.SAMTagAndValue createSAMTag()

deriveTypeFromKeyAndType

public static ReadTag deriveTypeFromKeyAndType(java.lang.String keyAndType,
                                               java.lang.Object value)

deriveTypeFromValue

public static ReadTag deriveTypeFromValue(java.lang.String key,
                                          java.lang.Object value)

getKey

public java.lang.String getKey()

compareTo

public int compareTo(ReadTag o)

Specified by:

compareTo in interface java.lang.Comparable<ReadTag>

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

getValue

public java.lang.Object getValue()

getType

public char getType()

getKeyAndType

public java.lang.String getKeyAndType()

getValueAsByteArray

public byte[] getValueAsByteArray()

restoreValueFromByteArray

public static java.lang.Object restoreValueFromByteArray(char type,
                                                         byte[] array)

getTagValueType

public static char getTagValueType(java.lang.Object value)

setIndex

public void setIndex(byte i)

getIndex

public byte getIndex()

writeSingleValue

public static byte[] writeSingleValue(byte tagType,
                                      java.lang.Object value,
                                      boolean isUnsignedArray)

readSingleValue

public static java.lang.Object readSingleValue(byte tagType,
                                               java.nio.ByteBuffer byteBuffer,
                                               ValidationStringency validationStringency)

main

public static void main(java.lang.String[] args)