Package htsjdk.samtools.cram.build
Class CramNormalizer
- java.lang.Object
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- htsjdk.samtools.cram.build.CramNormalizer
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public class CramNormalizer extends Object
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Constructor Summary
Constructors Constructor Description CramNormalizer(SAMFileHeader header, CRAMReferenceSource referenceSource)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static int
computeInsertSize(CramCompressionRecord firstEnd, CramCompressionRecord secondEnd)
The method is similar in semantics tocomputeInsertSize
but operates on CRAM native records instead of SAMRecord objects.void
normalize(ArrayList<CramCompressionRecord> records, byte[] ref, int refOffset_zeroBased, SubstitutionMatrix substitutionMatrix)
static void
restoreQualityScores(byte defaultQualityScore, List<CramCompressionRecord> records)
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Constructor Detail
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CramNormalizer
public CramNormalizer(SAMFileHeader header, CRAMReferenceSource referenceSource)
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Method Detail
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normalize
public void normalize(ArrayList<CramCompressionRecord> records, byte[] ref, int refOffset_zeroBased, SubstitutionMatrix substitutionMatrix)
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restoreQualityScores
public static void restoreQualityScores(byte defaultQualityScore, List<CramCompressionRecord> records)
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computeInsertSize
public static int computeInsertSize(CramCompressionRecord firstEnd, CramCompressionRecord secondEnd)
The method is similar in semantics tocomputeInsertSize
but operates on CRAM native records instead of SAMRecord objects.- Parameters:
firstEnd
- first mate of the pairsecondEnd
- second mate of the pair- Returns:
- template length
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