Package htsjdk.samtools.cram.structure
Class Slice
- java.lang.Object
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- htsjdk.samtools.cram.structure.Slice
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public class Slice extends Object
CRAM slice is a logical union of blocks into for example alignment slices.
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Field Summary
Fields Modifier and Type Field 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
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Constructor Summary
Constructors Constructor Description Slice()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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)
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Field Detail
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MULTI_REFERENCE
public static final int MULTI_REFERENCE
- See Also:
- Constant Field Values
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NO_ALIGNMENT_START
public static final int NO_ALIGNMENT_START
- See Also:
- Constant Field Values
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NO_ALIGNMENT_SPAN
public static final int NO_ALIGNMENT_SPAN
- See Also:
- Constant Field Values
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sequenceId
public int sequenceId
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alignmentStart
public int alignmentStart
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alignmentSpan
public int alignmentSpan
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nofRecords
public int nofRecords
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globalRecordCounter
public long globalRecordCounter
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nofBlocks
public int nofBlocks
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contentIDs
public int[] contentIDs
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embeddedRefBlockContentID
public int embeddedRefBlockContentID
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refMD5
public byte[] refMD5
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headerBlock
public Block headerBlock
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coreBlock
public Block coreBlock
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embeddedRefBlock
public Block embeddedRefBlock
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offset
public int offset
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containerOffset
public long containerOffset
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size
public int size
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index
public int index
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bases
public long bases
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sliceTags
public SAMBinaryTagAndValue sliceTags
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Method Detail
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validateRefMD5
public boolean validateRefMD5(byte[] ref)
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setRefMD5
public void setRefMD5(byte[] ref)
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getAttribute
public Object getAttribute(short tag)
Get tag value attached to the slice.- Parameters:
tag
- tag ID as a short integer as returned bySAMTagUtil.makeBinaryTag(java.lang.String)
- Returns:
- a value of the tag
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setAttribute
public void setAttribute(String tag, Object value)
Set a value for the tag.- Parameters:
tag
- tag ID as a short integer as returned bySAMTagUtil.makeBinaryTag(java.lang.String)
value
- tag value
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isMapped
public boolean isMapped()
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isMultiref
public boolean isMultiref()
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