htsjdk.samtools.cram.structure

Class Container

java.lang.Object

htsjdk.samtools.cram.structure.Container

public class Container
extends java.lang.Object

Notes: Container will construct a container out of as many CRAMCompressionRecords as it is handed, respecting only the maximum number of slices. The policy around how to break up lists of records into containers is enforced by ContainerFactory.

Constructor Summary

Constructors

Constructor and Description
Container(CompressionHeader compressionHeader, java.util.List<Slice> containerSlices, long containerByteOffset, long globalRecordCounter) Create a Container with a ReferenceContext derived from its Slices.
Container(ContainerHeader containerHeader, long containerByteOffset) Create a container for use by CramContainerHeaderIterator, which is only used to find the offsets within a CRAM stream where containers start.
Container(CRAMVersion cramVersion, java.io.InputStream inputStream, long containerByteOffset) Read a Container from a CRAM stream.

Method Summary

Modifier and Type	Method and Description
AlignmentContext	getAlignmentContext()
java.util.List<BAIEntry>	getBAIEntries(CompressorCache compressorCache) Retrieve the list of BAIEntry Index entries corresponding to this Container
CompressionHeader	getCompressionHeader()
long	getContainerByteOffset()
ContainerHeader	getContainerHeader()
java.util.List<CRAIEntry>	getCRAIEntries(CompressorCache compressorCache) Retrieve the list of CRAI Index entries corresponding to this Container
java.util.List<SAMRecord>	getSAMRecords(ValidationStringency validationStringency, CRAMReferenceRegion cramReferenceRegion, CompressorCache compressorCache, SAMFileHeader samFileHeader) Get SAMRecords from all Slices in this container.
java.util.List<Slice>	getSlices()
boolean	isEOF()
static SAMFileHeader	readSAMFileHeaderContainer(CRAMVersion cramVersion, java.io.InputStream inputStream, java.lang.String id) Reads the special container that contains the SAMFileHeader from a CRAM stream, and returns just the SAMFileHeader (we don't want to hand out the container since its not a real container in that it has no compression header block, slices, etc).
java.lang.String	toString()
int	write(CRAMVersion cramVersion, java.io.OutputStream outputStream) Writes a complete Container with it's header to a OutputStream.
static long	writeSAMFileHeaderContainer(CRAMVersion cramVersion, SAMFileHeader samFileHeader, java.io.OutputStream os) Write a SAMFileHeader container to a CRAM stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

Container

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

Create a Container with a ReferenceContext derived 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.

Parameters:

compressionHeader - the CRAM CompressionHeader to use for the Container

containerSlices - the Slices for the Container

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

globalRecordCounter - the global record count for the first record in this container

Throws:

CRAMException - for invalid Container states

Container

public Container(ContainerHeader containerHeader,
                 long containerByteOffset)

Create a container for use by CramContainerHeaderIterator, which is only used to find the offsets within a CRAM stream where containers start.

Parameters:

containerHeader - the container header for the container

containerByteOffset - the byte offset of this container in the containing stream

Container

public Container(CRAMVersion cramVersion,
                 java.io.InputStream inputStream,
                 long containerByteOffset)

Read a Container from a CRAM stream. This reads the container header and all slice blocks, but does not resolve the blocks into CRAMRecords, since we don't want to do that until its necessary (and it might not be if, for example, we're indexing the container).

Parameters:

cramVersion - CRAM version of the input stream

inputStream - input stream to read

containerByteOffset - byte offset within the stream of this container

Method Detail

write

public int write(CRAMVersion cramVersion,
                 java.io.OutputStream outputStream)

Writes a complete Container with it's header to a OutputStream.

Parameters:

cramVersion - the CRAM version to assume

outputStream - the stream to write to

Returns:

the number of bytes written out

readSAMFileHeaderContainer

public static SAMFileHeader readSAMFileHeaderContainer(CRAMVersion cramVersion,
                                                       java.io.InputStream inputStream,
                                                       java.lang.String id)

Reads the special container that contains the SAMFileHeader from a CRAM stream, and returns just the SAMFileHeader (we don't want to hand out the container since its not a real container in that it has no compression header block, slices, etc).

Parameters:

cramVersion - CRAM version being read

inputStream - stream from which to read the header container

id - id from the cram header, for error reporting

Returns:

the SAMFileHeader for this CRAM stream

writeSAMFileHeaderContainer

public static long writeSAMFileHeaderContainer(CRAMVersion cramVersion,
                                               SAMFileHeader samFileHeader,
                                               java.io.OutputStream os)

Write a SAMFileHeader container to a CRAM stream.

Parameters:

cramVersion - CRAM version being written.

samFileHeader - SAMFileHeader to write

os - stream to which the header container should be written

Returns:

the number of bytes written to the stream

getSAMRecords

public java.util.List<SAMRecord> getSAMRecords(ValidationStringency validationStringency,
                                               CRAMReferenceRegion cramReferenceRegion,
                                               CompressorCache compressorCache,
                                               SAMFileHeader samFileHeader)

Get SAMRecords from all Slices in this container. This is a 3 step process: 1) deserialize the slice blocks and create a list of CRAMRecords 2) Normalize the CRAMRecords 3) Convert the normalized CRAMRecords into SAMRecords

Parameters:

validationStringency - validation stringency to use (when reading tags)

cramReferenceRegion - reference region to use to restore bases

compressorCache - compressor cache to use for decompressing streams

samFileHeader - the SAMFileHeader for this CRAM stream (for resolving read groups)

Returns:

the SAMRecords from this container

getContainerHeader

public ContainerHeader getContainerHeader()

getCompressionHeader

public CompressionHeader getCompressionHeader()

getAlignmentContext

public AlignmentContext getAlignmentContext()

getContainerByteOffset

public long getContainerByteOffset()

getSlices

public java.util.List<Slice> getSlices()

isEOF

public boolean isEOF()

getCRAIEntries

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

Retrieve the list of CRAI Index entries corresponding to this Container

Returns:

the list of CRAI Index entries

getBAIEntries

public java.util.List<BAIEntry> getBAIEntries(CompressorCache compressorCache)

Retrieve the list of BAIEntry Index entries corresponding to this Container

Returns:

the list of BAIEntry Index entries

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object