htsjdk.samtools.cram.structure

Class ContainerHeader

java.lang.Object

htsjdk.samtools.cram.structure.ContainerHeader

public class ContainerHeader
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
ContainerHeader(AlignmentContext alignmentContext, int blockCount, int containerBlocksByteSize, int recordCount, long globalRecordCounter, long baseCount, java.util.List<java.lang.Integer> landmarks, int checksum) Create a ContainerHeader.
ContainerHeader(AlignmentContext alignmentContext, int blockCount, int recordCount, long globalRecordCounter, int baseCount) Create a Container from a partial set of values.
ContainerHeader(CRAMVersion cramVersion, java.io.InputStream inputStream) Create a container header from an InputStream.

Method Summary

Modifier and Type	Method and Description
AlignmentContext	getAlignmentContext()
long	getBaseCount()
int	getBlockCount()
int	getChecksum()
int	getContainerBlocksByteSize()
long	getGlobalRecordCounter()
java.util.List<java.lang.Integer>	getLandmarks()
int	getNumberOfRecords()
boolean	isEOF()
static ContainerHeader	makeSAMFileHeaderContainer(int containerBlocksByteSize) Create a ContainerHeader for a SAMFileHeader container.
void	setContainerBlocksByteSize(int containerBlocksByteSize)
void	setLandmarks(java.util.List<java.lang.Integer> landmarks)
java.lang.String	toString()
int	write(CRAMVersion cramVersion, java.io.OutputStream outputStream) Write CRAM Container (header only) out into the given OutputStream.

Methods inherited from class java.lang.Object

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

Constructor Detail

ContainerHeader

public ContainerHeader(AlignmentContext alignmentContext,
                       int blockCount,
                       int containerBlocksByteSize,
                       int recordCount,
                       long globalRecordCounter,
                       long baseCount,
                       java.util.List<java.lang.Integer> landmarks,
                       int checksum)

Create a ContainerHeader.

Parameters:

alignmentContext - the alignment context for this container

blockCount - block count for this container

containerBlocksByteSize -

recordCount - record count for this container

globalRecordCounter - global record count for this container

baseCount - base count for this container

landmarks - List of landmarks for this container (may be empty)

checksum -

ContainerHeader

public ContainerHeader(AlignmentContext alignmentContext,
                       int blockCount,
                       int recordCount,
                       long globalRecordCounter,
                       int baseCount)

Create a Container from a partial set of values. Used in cases where we don't yet have all of the values (such as landmarks, which, being stream offsets, can't be calculated until the container is written out to a stream).

Parameters:

alignmentContext - the alignment context for this container

blockCount - block count for this container

recordCount - record count for this container

globalRecordCounter - global record count for this container

baseCount - base count for this container

ContainerHeader

public ContainerHeader(CRAMVersion cramVersion,
                       java.io.InputStream inputStream)

Create a container header from an InputStream.

Parameters:

cramVersion - the CRAM version to assume

inputStream - the input stream from which to read

Method Detail

makeSAMFileHeaderContainer

public static ContainerHeader makeSAMFileHeaderContainer(int containerBlocksByteSize)

Create a ContainerHeader for a SAMFileHeader container.

Parameters:

containerBlocksByteSize - size of the SAMFileHeader block to be embedded in this container

getContainerBlocksByteSize

public int getContainerBlocksByteSize()

setContainerBlocksByteSize

public void setContainerBlocksByteSize(int containerBlocksByteSize)

getAlignmentContext

public AlignmentContext getAlignmentContext()

getNumberOfRecords

public int getNumberOfRecords()

getGlobalRecordCounter

public long getGlobalRecordCounter()

getBaseCount

public long getBaseCount()

getBlockCount

public int getBlockCount()

getLandmarks

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

setLandmarks

public void setLandmarks(java.util.List<java.lang.Integer> landmarks)

getChecksum

public int getChecksum()

write

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

Write CRAM Container (header only) out into the given OutputStream.

Parameters:

cramVersion - CRAM version

outputStream - the output stream to write the container header to

Returns:

number of bytes written out to the output stream

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

isEOF

public boolean isEOF()