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