Package htsjdk.samtools.cram.build
Class CRAMReferenceRegion
- java.lang.Object
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- htsjdk.samtools.cram.build.CRAMReferenceRegion
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public class CRAMReferenceRegion extends Object
A (cached) region of a reference. Maintains a CRAMReferenceSource for retrieving additional regions.
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Constructor Summary
Constructors Constructor Description CRAMReferenceRegion(CRAMReferenceSource cramReferenceSource, SAMFileHeader samFileHeader)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description byte[]
getCurrentReferenceBases()
byte[]
getReferenceBases(int referenceIndex)
Return the reference bases for the given reference index.void
setEmbeddedReference(byte[] embeddedReferenceBytes, int embeddedReferenceIndex)
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Constructor Detail
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CRAMReferenceRegion
public CRAMReferenceRegion(CRAMReferenceSource cramReferenceSource, SAMFileHeader samFileHeader)
- Parameters:
cramReferenceSource
-CRAMReferenceSource
to use to obtain reference basessamFileHeader
-SAMFileHeader
to use to resolve reference contig names to reference index
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Method Detail
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getCurrentReferenceBases
public byte[] getCurrentReferenceBases()
- Returns:
- the currently cached reference bases (may ne null)
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getReferenceBases
public byte[] getReferenceBases(int referenceIndex)
Return the reference bases for the given reference index.- Parameters:
referenceIndex
-- Returns:
- bases for the entire reference contig specifed by
referenceIndex
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setEmbeddedReference
public void setEmbeddedReference(byte[] embeddedReferenceBytes, int embeddedReferenceIndex)
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