Package htsjdk.samtools.cram.structure
Class ReadTag
- java.lang.Object
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- htsjdk.samtools.cram.structure.ReadTag
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- All Implemented Interfaces:
Comparable<ReadTag>
public class ReadTag extends Object implements Comparable<ReadTag>
CRAM counterpart ofSAMTag
. TODO: consider merging/dropping this class in favour of SAMTag or a SAMTag implementation.
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Field Summary
Fields Modifier and Type Field Description String
keyType3Bytes
int
keyType3BytesAsInt
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Constructor Summary
Constructors Constructor Description ReadTag(int id, byte[] dataAsByteArray, ValidationStringency validationStringency)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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)
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Field Detail
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keyType3Bytes
public String keyType3Bytes
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keyType3BytesAsInt
public int keyType3BytesAsInt
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Constructor Detail
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ReadTag
public ReadTag(int id, byte[] dataAsByteArray, ValidationStringency validationStringency)
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Method Detail
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name3BytesToInt
public static int name3BytesToInt(byte[] name)
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nameType3BytesToInt
public static int nameType3BytesToInt(String name, char type)
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intToNameType3Bytes
public static String intToNameType3Bytes(int value)
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intToNameType4Bytes
public static String intToNameType4Bytes(int value)
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createSAMTag
public SAMRecord.SAMTagAndValue createSAMTag()
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deriveTypeFromKeyAndType
public static ReadTag deriveTypeFromKeyAndType(String keyAndType, Object value)
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getKey
public String getKey()
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compareTo
public int compareTo(ReadTag o)
- Specified by:
compareTo
in interfaceComparable<ReadTag>
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getValue
public Object getValue()
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getKeyAndType
public String getKeyAndType()
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getValueAsByteArray
public byte[] getValueAsByteArray()
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setIndex
public void setIndex(byte i)
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getIndex
public byte getIndex()
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writeSingleValue
public static byte[] writeSingleValue(byte tagType, Object value, boolean isUnsignedArray)
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readSingleValue
public static Object readSingleValue(byte tagType, ByteBuffer byteBuffer, ValidationStringency validationStringency)
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