htsjdk.samtools.cram.structure

Class Container

java.lang.Object

htsjdk.samtools.cram.structure.Container

public class Container
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
int	alignmentSpan
int	alignmentStart
long	bases
int	blockCount
Block[]	blocks Container data
long	byteOffset
int	checksum
CompressionHeader	compressionHeader
int	containerBlocksByteSize The total length of all blocks in this container, of all types.
long	globalRecordCounter
int[]	landmarks Slice byte boundaries as offsets within this container, counted after the container header.
int	nofRecords

Constructor Summary

Constructors

Constructor and Description
Container(ReferenceContext refContext) Construct this Container by providing its ReferenceContext

Method Summary

Modifier and Type	Method and Description
void	distributeIndexingParametersToSlices() Populate the indexing parameters of this Container's slices Requires: valid landmarks and containerBlocksByteSize
java.util.List<CRAIEntry>	getCRAIEntries() Retrieve the list of CRAI Index entries corresponding to this Container
ReferenceContext	getReferenceContext()
Slice[]	getSlices()
java.util.Map<ReferenceContext,AlignmentSpan>	getSpans(ValidationStringency validationStringency) Iterate through all of this container's Slices to derive a map of reference sequence IDs to AlignmentSpans.
static Container	initializeFromSlices(java.util.List<Slice> containerSlices, CompressionHeader compressionHeader, long containerByteOffset) Derive the container's ReferenceContext from its Slices.
boolean	isEOF()
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

containerBlocksByteSize

public int containerBlocksByteSize

The total length of all blocks in this container, of all types. Equal to the total length of this container, minus the Container Header.

See Also:

BlockContentType

alignmentStart

public int alignmentStart

alignmentSpan

public int alignmentSpan

nofRecords

public int nofRecords

globalRecordCounter

public long globalRecordCounter

bases

public long bases

blockCount

public int blockCount

landmarks

public int[] landmarks

Slice byte boundaries as offsets within this container, counted after the container header. The start of the compression header has offset 0. Equal to Slice.byteOffsetFromCompressionHeaderStart. As an example, suppose we have: - landmarks[0] = 9000 - landmarks[1] = 109000 - containerBlocksByteSize = 123456 We therefore know: - the compression header size = 9000 - Slice 0 has offset 9000 and size 100000 (109000 - 9000) - Slice 1 has offset 109000 and size 14456 (123456 - 109000)

checksum

public int checksum

blocks

public Block[] blocks

Container data

compressionHeader

public CompressionHeader compressionHeader

byteOffset

public long byteOffset

Constructor Detail

Container

public Container(ReferenceContext refContext)

Construct this Container by providing its ReferenceContext

Parameters:

refContext - the reference context associated with this container

Method Detail

getSlices

public Slice[] getSlices()

getReferenceContext

public ReferenceContext getReferenceContext()

initializeFromSlices

public static Container initializeFromSlices(java.util.List<Slice> containerSlices,
                                             CompressionHeader compressionHeader,
                                             long containerByteOffset)

Derive the container's ReferenceContext from its Slices. A Single Reference Container contains only Single Reference Slices mapped to the same reference. - set the Container's ReferenceContext to be the same as those slices - set the Container's Alignment Start and Span to cover all slices A Multiple Reference Container contains only Multiple Reference Slices. - set the Container's ReferenceContext to MULTIPLE_REFERENCE_CONTEXT - unset the Container's Alignment Start and Span An Unmapped Container contains only Unmapped Slices. - set the Container's ReferenceContext to UNMAPPED_UNPLACED_CONTEXT - unset the Container's Alignment Start and Span Any other combination is invalid. TODO for general Container refactoring: make this part of construction

Parameters:

containerSlices - the constituent Slices of the Container

compressionHeader - the CRAM CompressionHeader to assign to the Container

containerByteOffset - the Container's byte offset from the start of the stream

Returns:

the initialized Container

Throws:

CRAMException - for invalid Container states

distributeIndexingParametersToSlices

public void distributeIndexingParametersToSlices()

Populate the indexing parameters of this Container's slices Requires: valid landmarks and containerBlocksByteSize

Throws:

CRAMException - when the Container is in an invalid state

getCRAIEntries

public java.util.List<CRAIEntry> getCRAIEntries()

Retrieve the list of CRAI Index entries corresponding to this Container

Returns:

the list of CRAI Index entries

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isEOF

public boolean isEOF()

getSpans

public java.util.Map<ReferenceContext,AlignmentSpan> getSpans(ValidationStringency validationStringency)

Iterate through all of this container's Slices to derive a map of reference sequence IDs to AlignmentSpans. Used to create BAI Indexes.

Parameters:

validationStringency - stringency for validating records, passed to Slice.getMultiRefAlignmentSpans(CompressionHeader, ValidationStringency)

Returns:

the map of map of reference sequence IDs to AlignmentSpans.