Package htsjdk.samtools.cram.structure

Class ReadTag

java.lang.Object

htsjdk.samtools.cram.structure.ReadTag

All Implemented Interfaces:

Comparable<ReadTag>

public class ReadTag
extends Object
implements Comparable<ReadTag>

CRAM counterpart of SAMTag.

Field Summary

Fields

Modifier and Type	Field	Description
String	keyType3Bytes
int	keyType3BytesAsInt

Constructor Summary

Constructors

Constructor	Description
ReadTag(int id, byte[] dataAsByteArray, ValidationStringency validationStringency)

Method Summary

Modifier and Type	Method	Description
int	compareTo(ReadTag o)
SAMRecord.SAMTagAndValue	createSAMTag()
static ReadTag	deriveTypeFromKeyAndType(String keyAndType, Object value)
static ReadTag	deriveTypeFromValue(String key, Object value)
boolean	equals(Object o)
byte	getIndex()
String	getKey()
String	getKeyAndType()
Object	getValue()
byte[]	getValueAsByteArray()
int	hashCode()
static String	intToNameType3Bytes(int value)
static String	intToNameType4Bytes(int value)
static int	name3BytesToInt(byte[] name)
static int	nameType3BytesToInt(String name, char type)
static Object	readSingleValue(byte tagType, ByteBuffer byteBuffer, ValidationStringency validationStringency)
void	setIndex(byte i)
static byte[]	writeSingleValue(byte tagType, Object value, boolean isUnsignedArray)

Methods inherited from class java.lang.Object

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

Field Details

keyType3Bytes

public String keyType3Bytes

keyType3BytesAsInt

public int keyType3BytesAsInt

Constructor Details

ReadTag

public ReadTag(int id,
 byte[] dataAsByteArray,
 ValidationStringency validationStringency)

Method Details

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)

createSAMTag

public SAMRecord.SAMTagAndValue createSAMTag()

deriveTypeFromKeyAndType

public static ReadTag deriveTypeFromKeyAndType(String keyAndType,
 Object value)

deriveTypeFromValue

public static ReadTag deriveTypeFromValue(String key,
 Object value)

getKey

public String getKey()

compareTo

public int compareTo(ReadTag o)

Specified by:

compareTo in interface Comparable<ReadTag>

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)

readSingleValue

public static Object readSingleValue(byte tagType,
 ByteBuffer byteBuffer,
 ValidationStringency validationStringency)

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object