Package htsjdk.samtools.cram.ref
Interface CRAMReferenceSource
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- All Known Implementing Classes:
CRAMLazyReferenceSource
,ReferenceSource
public interface CRAMReferenceSource
Interface used to supply a reference source when reading CRAM files.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description byte[]
getReferenceBases(SAMSequenceRecord sequenceRecord, boolean tryNameVariants)
getReferenceBases
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Method Detail
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getReferenceBases
byte[] getReferenceBases(SAMSequenceRecord sequenceRecord, boolean tryNameVariants)
getReferenceBases- Parameters:
sequenceRecord
- the SAMSequenceRecord identifying the reference being requestedtryNameVariants
- if true, attempt to match the requested sequence name against the reference by using common name variations, such as adding or removing a leading "chr" prefix from the requested name. if false, use exact match- Returns:
- the upper cased, normalized (see
Utils.normalizeBase(byte)
) bases representing the requested sequence, or null if the sequence cannot be found
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