public class Slice extends Object
Modifier and Type | Field and Description |
---|---|
int |
alignmentSpan |
int |
alignmentStart |
long |
bases |
long |
containerOffset |
int[] |
contentIDs |
Block |
coreBlock |
Block |
embeddedRefBlock |
int |
embeddedRefBlockContentID |
Map<Integer,Block> |
external |
long |
globalRecordCounter |
Block |
headerBlock |
int |
index |
static int |
MULTI_REFERENCE |
static int |
NO_ALIGNMENT_SPAN |
static int |
NO_ALIGNMENT_START |
int |
nofBlocks |
int |
nofRecords |
int |
offset |
byte[] |
refMD5 |
int |
sequenceId |
int |
size |
SAMBinaryTagAndValue |
sliceTags |
Constructor and Description |
---|
Slice() |
Modifier and Type | Method and Description |
---|---|
Object |
getAttribute(short tag)
Get tag value attached to the slice.
|
boolean |
isMapped() |
boolean |
isMultiref() |
void |
setAttribute(String tag,
Object value)
Set a value for the tag.
|
void |
setRefMD5(byte[] ref) |
void |
setUnsignedArrayAttribute(String tag,
Object value) |
String |
toString() |
boolean |
validateRefMD5(byte[] ref) |
public static final int MULTI_REFERENCE
public static final int NO_ALIGNMENT_START
public static final int NO_ALIGNMENT_SPAN
public int sequenceId
public int alignmentStart
public int alignmentSpan
public int nofRecords
public long globalRecordCounter
public int nofBlocks
public int[] contentIDs
public int embeddedRefBlockContentID
public byte[] refMD5
public Block headerBlock
public Block coreBlock
public Block embeddedRefBlock
public int offset
public long containerOffset
public int size
public int index
public long bases
public SAMBinaryTagAndValue sliceTags
public boolean validateRefMD5(byte[] ref)
public void setRefMD5(byte[] ref)
public Object getAttribute(short tag)
tag
- tag ID as a short integer as returned by SAMTagUtil.makeBinaryTag(java.lang.String)
public void setAttribute(String tag, Object value)
tag
- tag ID as a short integer as returned by SAMTagUtil.makeBinaryTag(java.lang.String)
value
- tag valuepublic boolean isMapped()
public boolean isMultiref()