public class CramNormalizer
extends java.lang.Object
Constructor and Description |
---|
CramNormalizer(SAMFileHeader header,
ReferenceSource referenceSource) |
Modifier and Type | Method and Description |
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static int |
computeInsertSize(CramCompressionRecord firstEnd,
CramCompressionRecord secondEnd)
The method is similar in semantics to
computeInsertSize but operates on CRAM native records instead of
SAMRecord objects. |
void |
normalize(java.util.ArrayList<CramCompressionRecord> records,
byte[] ref,
int refOffset_zeroBased,
SubstitutionMatrix substitutionMatrix) |
static void |
restoreQualityScores(byte defaultQualityScore,
java.util.List<CramCompressionRecord> records) |
public CramNormalizer(SAMFileHeader header, ReferenceSource referenceSource)
public void normalize(java.util.ArrayList<CramCompressionRecord> records, byte[] ref, int refOffset_zeroBased, SubstitutionMatrix substitutionMatrix)
public static void restoreQualityScores(byte defaultQualityScore, java.util.List<CramCompressionRecord> records)
public static int computeInsertSize(CramCompressionRecord firstEnd, CramCompressionRecord secondEnd)
computeInsertSize
but operates on CRAM native records instead of
SAMRecord objects.firstEnd
- first mate of the pairsecondEnd
- second mate of the pair