Package htsjdk.samtools.cram.structure
Class ContainerHeader
- java.lang.Object
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- htsjdk.samtools.cram.structure.ContainerHeader
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public class ContainerHeader extends Object
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Constructor Summary
Constructors Constructor Description ContainerHeader(CRAMVersion cramVersion, InputStream inputStream)
Create a container header from anInputStream
.ContainerHeader(AlignmentContext alignmentContext, int blockCount, int containerBlocksByteSize, int recordCount, long globalRecordCounter, long baseCount, List<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.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description AlignmentContext
getAlignmentContext()
long
getBaseCount()
int
getBlockCount()
int
getChecksum()
int
getContainerBlocksByteSize()
long
getGlobalRecordCounter()
List<Integer>
getLandmarks()
int
getNumberOfRecords()
boolean
isEOF()
static ContainerHeader
makeSAMFileHeaderContainer(int containerBlocksByteSize)
Create a ContainerHeader for a SAMFileHeader container.void
setContainerBlocksByteSize(int containerBlocksByteSize)
void
setLandmarks(List<Integer> landmarks)
String
toString()
int
write(CRAMVersion cramVersion, OutputStream outputStream)
Write CRAMContainer
(header only) out into the givenOutputStream
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Constructor Detail
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ContainerHeader
public ContainerHeader(AlignmentContext alignmentContext, int blockCount, int containerBlocksByteSize, int recordCount, long globalRecordCounter, long baseCount, List<Integer> landmarks, int checksum)
Create a ContainerHeader.- Parameters:
alignmentContext
- the alignment context for this containerblockCount
- block count for this containercontainerBlocksByteSize
-recordCount
- record count for this containerglobalRecordCounter
- global record count for this containerbaseCount
- base count for this containerlandmarks
- List of landmarks for this container (may be empty)checksum
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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 containerblockCount
- block count for this containerrecordCount
- record count for this containerglobalRecordCounter
- global record count for this containerbaseCount
- base count for this container
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ContainerHeader
public ContainerHeader(CRAMVersion cramVersion, InputStream inputStream)
Create a container header from anInputStream
.- Parameters:
cramVersion
- the CRAM version to assumeinputStream
- the input stream from which to read
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Method Detail
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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
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getContainerBlocksByteSize
public int getContainerBlocksByteSize()
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setContainerBlocksByteSize
public void setContainerBlocksByteSize(int containerBlocksByteSize)
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getAlignmentContext
public AlignmentContext getAlignmentContext()
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getNumberOfRecords
public int getNumberOfRecords()
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getGlobalRecordCounter
public long getGlobalRecordCounter()
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getBaseCount
public long getBaseCount()
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getBlockCount
public int getBlockCount()
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getChecksum
public int getChecksum()
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write
public int write(CRAMVersion cramVersion, OutputStream outputStream)
Write CRAMContainer
(header only) out into the givenOutputStream
.- Parameters:
cramVersion
- CRAM versionoutputStream
- the output stream to write the container header to- Returns:
- number of bytes written out to the output stream
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isEOF
public boolean isEOF()
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