Slice (htsjdk 2.21.1 API)

java.lang.Object
- htsjdk.samtools.cram.structure.Slice

```
public class Slice
extends java.lang.Object
```
CRAM slice is a logical union of blocks into for example alignment slices.

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`alignmentSpan`
`int`	`alignmentStart`
`long`	`bases`
`int`	`byteOffsetFromCompressionHeaderStart` The Slice's offset in bytes from the beginning of the Container's Compression Header (or the end of the Container Header), equal to `Container.landmarks` Used by BAI and CRAI indexing
`int`	`byteSize` The Slice's size in bytes Used by CRAI indexing only
`long`	`containerByteOffset` The Slice's Container's offset in bytes from the beginning of the stream equal to `Container.byteOffset` Used by BAI and CRAI indexing
`int[]`	`contentIDs`
`Block`	`coreBlock`
`Block`	`embeddedRefBlock`
`int`	`embeddedRefBlockContentID`
`java.util.Map<java.lang.Integer,Block>`	`external`
`long`	`globalRecordCounter`
`Block`	`headerBlock`
`int`	`index` The Slice's index number within its Container Used by BAI indexing only
`int`	`mappedReadsCount`
`static int`	`NO_ALIGNMENT_END`
`static int`	`NO_ALIGNMENT_SPAN`
`static int`	`NO_ALIGNMENT_START`
`int`	`nofBlocks`
`int`	`nofRecords`
`byte[]`	`refMD5`
`SAMBinaryTagAndValue`	`sliceTags`
`static int`	`UNINITIALIZED_INDEXING_PARAMETER`
`int`	`unmappedReadsCount`
`int`	`unplacedReadsCount`

Constructor Summary

Constructors
Constructor and Description

Slice(ReferenceContext refContext)
Construct this Slice by providing its ReferenceContext

Constructors
Constructor and Description
`Slice(ReferenceContext refContext)` Construct this Slice by providing its `ReferenceContext`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`baiIndexInitializationCheck()` Confirm that we have initialized the 3 BAI index parameters: byteOffsetFromCompressionHeaderStart, containerByteOffset, and index
`static Slice`	`buildSlice(java.util.List<CramCompressionRecord> records, CompressionHeader header)` Create a single Slice from CRAM Compression Records and a Compression Header.
`CramRecordReader`	`createCramRecordReader(CompressionHeader header, ValidationStringency validationStringency)` Initialize a Cram Record Reader from a Slice
`java.lang.Object`	`getAttribute(short tag)` Get tag value attached to the slice.
`java.util.List<CRAIEntry>`	`getCRAIEntries(CompressionHeader compressionHeader)` Generate a CRAI Index entry from this Slice and other container parameters, splitting Multiple Reference slices into constituent reference sequence entries.
`java.util.Map<ReferenceContext,AlignmentSpan>`	`getMultiRefAlignmentSpans(CompressionHeader header, ValidationStringency validationStringency)` Uses a Multiple Reference Slice Alignment Reader to determine the Reference Spans of a Slice.
`ReferenceContext`	`getReferenceContext()`
`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)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - NO_ALIGNMENT_START
```
public static final int NO_ALIGNMENT_START
```
    See Also:
    
    Constant Field Values
  - NO_ALIGNMENT_SPAN
```
public static final int NO_ALIGNMENT_SPAN
```
    See Also:
    
    Constant Field Values
  - NO_ALIGNMENT_END
```
public static final int NO_ALIGNMENT_END
```
    See Also:
    
    Constant Field Values
  - alignmentStart
```
public int alignmentStart
```
  - alignmentSpan
```
public int alignmentSpan
```
  - nofRecords
```
public int nofRecords
```
  - globalRecordCounter
```
public long globalRecordCounter
```
  - nofBlocks
```
public int nofBlocks
```
  - contentIDs
```
public int[] contentIDs
```
  - embeddedRefBlockContentID
```
public int embeddedRefBlockContentID
```
  - refMD5
```
public byte[] refMD5
```
  - headerBlock
```
public Block headerBlock
```
  - coreBlock
```
public Block coreBlock
```
  - embeddedRefBlock
```
public Block embeddedRefBlock
```
  - external
```
public java.util.Map<java.lang.Integer,Block> external
```
  - UNINITIALIZED_INDEXING_PARAMETER
```
public static final int UNINITIALIZED_INDEXING_PARAMETER
```
    See Also:
    
    Constant Field Values
  - byteOffsetFromCompressionHeaderStart
```
public int byteOffsetFromCompressionHeaderStart
```
    The Slice's offset in bytes from the beginning of the Container's Compression Header (or the end of the Container Header), equal to Container.landmarks Used by BAI and CRAI indexing
  - containerByteOffset
```
public long containerByteOffset
```
    The Slice's Container's offset in bytes from the beginning of the stream equal to Container.byteOffset Used by BAI and CRAI indexing
  - byteSize
```
public int byteSize
```
    The Slice's size in bytes Used by CRAI indexing only
  - index
```
public int index
```
    The Slice's index number within its Container Used by BAI indexing only
  - bases
```
public long bases
```
  - sliceTags
```
public SAMBinaryTagAndValue sliceTags
```
  - mappedReadsCount
```
public int mappedReadsCount
```
  - unmappedReadsCount
```
public int unmappedReadsCount
```
  - unplacedReadsCount
```
public int unplacedReadsCount
```
- Constructor Detail
  - Slice
```
public Slice(ReferenceContext refContext)
```
    Construct this Slice by providing its ReferenceContext
    
    Parameters:
    
    refContext - the reference context associated with this slice
- Method Detail
  - getReferenceContext
```
public ReferenceContext getReferenceContext()
```
  - baiIndexInitializationCheck
```
public void baiIndexInitializationCheck()
```
    Confirm that we have initialized the 3 BAI index parameters: byteOffsetFromCompressionHeaderStart, containerByteOffset, and index
  - validateRefMD5
```
public boolean validateRefMD5(byte[] ref)
```
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - setRefMD5
```
public void setRefMD5(byte[] ref)
```
  - getAttribute
```
public java.lang.Object getAttribute(short tag)
```
    Get tag value attached to the slice.
    
    Parameters:
    
    tag - tag ID as a short integer as returned by SAMTag.makeBinaryTag(String)
    
    Returns:
    
    a value of the tag
  - setAttribute
```
public void setAttribute(java.lang.String tag,
                         java.lang.Object value)
```
    Set a value for the tag.
    
    Parameters:
    
    tag - tag ID as a short integer as returned by SAMTag.makeBinaryTag(String)
    
    value - tag value
  - setUnsignedArrayAttribute
```
public void setUnsignedArrayAttribute(java.lang.String tag,
                                      java.lang.Object value)
```
  - createCramRecordReader
```
public CramRecordReader createCramRecordReader(CompressionHeader header,
                                               ValidationStringency validationStringency)
```
    Initialize a Cram Record Reader from a Slice
    
    Parameters:
    
    header - the associated Cram Compression Header
    
    validationStringency - how strict to be when reading this CRAM record
  - getMultiRefAlignmentSpans
```
public java.util.Map<ReferenceContext,AlignmentSpan> getMultiRefAlignmentSpans(CompressionHeader header,
                                                                               ValidationStringency validationStringency)
```
    Uses a Multiple Reference Slice Alignment Reader to determine the Reference Spans of a Slice. The intended use is for CRAI indexing.
    
    Parameters:
    
    header - the associated Cram Compression Header
    
    validationStringency - how strict to be when reading CRAM records
  - getCRAIEntries
```
public java.util.List<CRAIEntry> getCRAIEntries(CompressionHeader compressionHeader)
```
    Generate a CRAI Index entry from this Slice and other container parameters, splitting Multiple Reference slices into constituent reference sequence entries.
    
    Parameters:
    
    compressionHeader - the enclosing Container's CompressionHeader
    
    Returns:
    
    a list of CRAI Index Entries derived from this Slice
  - buildSlice
```
public static Slice buildSlice(java.util.List<CramCompressionRecord> records,
                               CompressionHeader header)
```
    Create a single Slice from CRAM Compression Records and a Compression Header. The caller is responsible for appropriate subdivision of records into containers and slices.
    
    Parameters:
    
    records - input CRAM Compression Records
    
    header - the enclosing Container's Compression Header
    
    Returns:
    
    a Slice corresponding to the given records

Class Slice

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

NO_ALIGNMENT_START

NO_ALIGNMENT_SPAN

NO_ALIGNMENT_END

alignmentStart

alignmentSpan

nofRecords

globalRecordCounter

nofBlocks

contentIDs

embeddedRefBlockContentID

refMD5

headerBlock

coreBlock

embeddedRefBlock

external

UNINITIALIZED_INDEXING_PARAMETER

byteOffsetFromCompressionHeaderStart

containerByteOffset

byteSize

index

bases

sliceTags

mappedReadsCount

unmappedReadsCount

unplacedReadsCount

Constructor Detail

Slice

Method Detail

getReferenceContext

baiIndexInitializationCheck

validateRefMD5

toString

setRefMD5

getAttribute

setAttribute

setUnsignedArrayAttribute

createCramRecordReader

getMultiRefAlignmentSpans

getCRAIEntries

buildSlice