public class CramNormalizer extends Object
| Constructor | Description |
|---|---|
CramNormalizer(SAMFileHeader header,
CRAMReferenceSource referenceSource) |
| Modifier and Type | Method | Description |
|---|---|---|
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(ArrayList<CramCompressionRecord> records,
byte[] ref,
int refOffset_zeroBased,
SubstitutionMatrix substitutionMatrix) |
|
static void |
restoreQualityScores(byte defaultQualityScore,
List<CramCompressionRecord> records) |
public CramNormalizer(SAMFileHeader header, CRAMReferenceSource referenceSource)
public void normalize(ArrayList<CramCompressionRecord> records, byte[] ref, int refOffset_zeroBased, SubstitutionMatrix substitutionMatrix)
public static void restoreQualityScores(byte defaultQualityScore,
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