htsjdk.samtools.cram.build

Class CramNormalizer

java.lang.Object

htsjdk.samtools.cram.build.CramNormalizer

public class CramNormalizer
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
CramNormalizer(SAMFileHeader header, CRAMReferenceSource referenceSource)

Method Summary

Modifier and Type	Method and 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(java.util.ArrayList<CramCompressionRecord> records, byte[] ref, int refOffset_zeroBased, SubstitutionMatrix substitutionMatrix)
static void	restoreQualityScores(byte defaultQualityScore, java.util.List<CramCompressionRecord> records)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CramNormalizer

public CramNormalizer(SAMFileHeader header,
                      CRAMReferenceSource referenceSource)

Method Detail

normalize

public void normalize(java.util.ArrayList<CramCompressionRecord> records,
                      byte[] ref,
                      int refOffset_zeroBased,
                      SubstitutionMatrix substitutionMatrix)

restoreQualityScores

public static void restoreQualityScores(byte defaultQualityScore,
                                        java.util.List<CramCompressionRecord> records)

computeInsertSize

public 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.

Parameters:

firstEnd - first mate of the pair

secondEnd - second mate of the pair

Returns:

template length