htsjdk.samtools.cram.structure

Class SliceBlocks

java.lang.Object

htsjdk.samtools.cram.structure.SliceBlocks

public class SliceBlocks
extends java.lang.Object

Manage the (logical) set of blocks that constitute a Slice, not including the Slice header block, which is managed by Slice. Prevents duplicate blocks (blocks with non-unique content ID) or illogical blocks (i.e., setting a core block that is not of type core block, or an external block that is not an external block) from being added.

Constructor Summary

Constructors

Constructor and Description
SliceBlocks(Block coreBlock, java.util.List<Block> externalBlocks) Create a new SliceBlocks object from a core block and one or more external blocks.
SliceBlocks(CRAMVersion cramVersion, int numberOfBlocks, java.io.InputStream inputStream) Read the set of blocks that make up a slice from a CRAM stream.

Method Summary

Modifier and Type	Method and Description
Block	getCoreBlock() Return the core block for this Slice.
Block	getExternalBlock(java.lang.Integer contentID) Get the external block corresponding to a contentID.
java.util.List<java.lang.Integer>	getExternalContentIDs() Return a list of external content IDs.
int	getNumberOfExternalBlocks() Number of external locks present in this SliceBlocks object (does not include the core block).
void	writeBlocks(CRAMVersion cramVersion, java.io.OutputStream outputStream) Write the coreBlock and each external block out to a CRAM stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

SliceBlocks

public SliceBlocks(Block coreBlock,
                   java.util.List<Block> externalBlocks)

Create a new SliceBlocks object from a core block and one or more external blocks.

Parameters:

coreBlock - the core block for the Slice, may not be null

externalBlocks - the external blocks for this Slice, may not be null and must contain a least one block

SliceBlocks

public SliceBlocks(CRAMVersion cramVersion,
                   int numberOfBlocks,
                   java.io.InputStream inputStream)

Read the set of blocks that make up a slice from a CRAM stream.

Parameters:

cramVersion - CRAM version being read

numberOfBlocks - number of blocks to consume from the stream

inputStream - stream to consume

Method Detail

getCoreBlock

public Block getCoreBlock()

Return the core block for this Slice. May be null.

getExternalBlock

public Block getExternalBlock(java.lang.Integer contentID)

Get the external block corresponding to a contentID.

Parameters:

contentID - contentID identifying the external block

Returns:

external block for the contentID. May be null.

getExternalContentIDs

public java.util.List<java.lang.Integer> getExternalContentIDs()

Return a list of external content IDs. May be empty. For each content ID returned, the corresponding external block can be obtained using getExternalBlock(java.lang.Integer).

Returns:

list of external content IDs

getNumberOfExternalBlocks

public int getNumberOfExternalBlocks()

Number of external locks present in this SliceBlocks object (does not include the core block).

Returns:

number of external blocks, including any embedded reference block, but excluding the core block

writeBlocks

public void writeBlocks(CRAMVersion cramVersion,
                        java.io.OutputStream outputStream)

Write the coreBlock and each external block out to a CRAM stream. There is no predefined order that must be honored, since each block is identified by a unique contentID.

Parameters:

cramVersion - CRAM major version being written

outputStream - stream to write blocks to