htsjdk.samtools.cram.build

Class Sam2CramRecordFactory

java.lang.Object

htsjdk.samtools.cram.build.Sam2CramRecordFactory

public class Sam2CramRecordFactory
extends java.lang.Object

Field Summary

Fields

Modifier and Type	Field and Description
boolean	captureAllTags
java.util.Set<java.lang.String>	captureTags
static byte	ignorePositionsWithQualityScore
java.util.Set<java.lang.String>	ignoreTags
boolean	preserveReadNames
static java.lang.String	UNKNOWN_READ_GROUP_ID
static java.lang.String	UNKNOWN_READ_GROUP_SAMPLE
static byte	unsetQualityScore

Constructor Summary

Constructors

Constructor and Description
Sam2CramRecordFactory(byte[] refBases, SAMFileHeader samFileHeader, Version version)

Method Summary

Methods

Modifier and Type	Method and Description
CramCompressionRecord	createCramRecord(SAMRecord record)
long	getBaseCount()
long	getFeatureCount()
long	getLandedRefMaskScores()
long	getLandedTotalScores()
java.util.Map<java.lang.String,java.lang.Integer>	getReadGroupMap()
byte[]	getRefBases()
byte[]	getRefSNPs()
void	setRefBases(byte[] refBases)
void	setRefSNPs(byte[] refSNPs)

Methods inherited from class java.lang.Object

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

Field Detail

UNKNOWN_READ_GROUP_ID

public static final java.lang.String UNKNOWN_READ_GROUP_ID

See Also:

Constant Field Values

UNKNOWN_READ_GROUP_SAMPLE

public static final java.lang.String UNKNOWN_READ_GROUP_SAMPLE

See Also:

Constant Field Values

unsetQualityScore

public static final byte unsetQualityScore

See Also:

Constant Field Values

ignorePositionsWithQualityScore

public static final byte ignorePositionsWithQualityScore

See Also:

Constant Field Values

captureAllTags

public boolean captureAllTags

preserveReadNames

public boolean preserveReadNames

captureTags

public final java.util.Set<java.lang.String> captureTags

ignoreTags

public final java.util.Set<java.lang.String> ignoreTags

Constructor Detail

Sam2CramRecordFactory

public Sam2CramRecordFactory(byte[] refBases,
                     SAMFileHeader samFileHeader,
                     Version version)

Method Detail

createCramRecord

public CramCompressionRecord createCramRecord(SAMRecord record)

getLandedRefMaskScores

public long getLandedRefMaskScores()

getLandedTotalScores

public long getLandedTotalScores()

getRefBases

public byte[] getRefBases()

setRefBases

public void setRefBases(byte[] refBases)

getRefSNPs

public byte[] getRefSNPs()

setRefSNPs

public void setRefSNPs(byte[] refSNPs)

getReadGroupMap

public java.util.Map<java.lang.String,java.lang.Integer> getReadGroupMap()

getBaseCount

public long getBaseCount()

getFeatureCount

public long getFeatureCount()