picard.arrays.illumina

Class IlluminaManifestRecord

java.lang.Object

picard.arrays.illumina.IlluminaManifestRecord

Direct Known Subclasses:

Build37ExtendedIlluminaManifestRecord

public class IlluminaManifestRecord
extends java.lang.Object

A class to represent a record (line) from an Illumina Manifest [Assay] entry

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
protected static class	IlluminaManifestRecord.IlluminaStrand

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ILLUMINA_FLAGGED_BAD_CHR

Method Summary

Modifier and Type	Method and Description
java.lang.String	getAddressAId()
java.lang.String	getAddressBId()
java.lang.String	getAlleleAProbeSeq()
java.lang.String	getAlleleBProbeSeq()
int	getBeadSetId()
java.lang.String	getChr()
java.lang.String	getExpClusters()
java.lang.String	getGenomeBuild()
java.lang.String	getHgGenomeBuild()
java.lang.String	getIlmnId()
IlluminaManifestRecord.IlluminaStrand	getIlmnStrand()
int	getIndex()
boolean	getIntensityOnly()
java.lang.String	getLine()
java.lang.String	getMajorGenomeBuild()
java.lang.String	getName()
java.lang.String	getPloidy()
int	getPosition()
htsjdk.tribble.annotation.Strand	getRefStrand()
java.lang.String	getSnp()
java.lang.String	getSource()
java.lang.String	getSourceSeq()
IlluminaManifestRecord.IlluminaStrand	getSourceStrand()
java.lang.String	getSourceVersion()
java.lang.String	getSpecies()
java.lang.String	getTopGenomicSeq()
boolean	isAmbiguous()
boolean	isIndel()
boolean	isSnp()
void	setHgGenomeBuild(java.lang.String hgGenomeBuild)

Methods inherited from class java.lang.Object

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

Field Detail

ILLUMINA_FLAGGED_BAD_CHR

public static final java.lang.String ILLUMINA_FLAGGED_BAD_CHR

See Also:

Constant Field Values

Method Detail

getLine

public java.lang.String getLine()

getIlmnId

public java.lang.String getIlmnId()

getName

public java.lang.String getName()

getIlmnStrand

public IlluminaManifestRecord.IlluminaStrand getIlmnStrand()

getSnp

public java.lang.String getSnp()

isIndel

public boolean isIndel()

isAmbiguous

public boolean isAmbiguous()

isSnp

public boolean isSnp()

getAddressAId

public java.lang.String getAddressAId()

getAlleleAProbeSeq

public java.lang.String getAlleleAProbeSeq()

getAddressBId

public java.lang.String getAddressBId()

getAlleleBProbeSeq

public java.lang.String getAlleleBProbeSeq()

getGenomeBuild

public java.lang.String getGenomeBuild()

getMajorGenomeBuild

public java.lang.String getMajorGenomeBuild()

getHgGenomeBuild

public java.lang.String getHgGenomeBuild()

setHgGenomeBuild

public void setHgGenomeBuild(java.lang.String hgGenomeBuild)

getChr

public java.lang.String getChr()

getPosition

public int getPosition()

getPloidy

public java.lang.String getPloidy()

getSpecies

public java.lang.String getSpecies()

getSource

public java.lang.String getSource()

getSourceVersion

public java.lang.String getSourceVersion()

getSourceStrand

public IlluminaManifestRecord.IlluminaStrand getSourceStrand()

getSourceSeq

public java.lang.String getSourceSeq()

getTopGenomicSeq

public java.lang.String getTopGenomicSeq()

getBeadSetId

public int getBeadSetId()

getExpClusters

public java.lang.String getExpClusters()

getRefStrand

public htsjdk.tribble.annotation.Strand getRefStrand()

getIntensityOnly

public boolean getIntensityOnly()

getIndex

public int getIndex()