java.lang.Object
- picard.arrays.illumina.IlluminaManifestRecord
- - picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord

```
public class Build37ExtendedIlluminaManifestRecord
extends IlluminaManifestRecord
```
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry

Nested Class Summary

Nested Classes
Modifier and Type Class Description

protected static class Build37ExtendedIlluminaManifestRecord.Flag
- Nested classes/interfaces inherited from class picard.arrays.illumina.IlluminaManifestRecord
  IlluminaManifestRecord.IlluminaStrand

Field Summary
- Fields inherited from class picard.arrays.illumina.IlluminaManifestRecord
  ILLUMINA_FLAGGED_BAD_CHR

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`htsjdk.variant.variantcontext.Allele`	`getAlleleA()`
`htsjdk.variant.variantcontext.Allele`	`getAlleleB()`
`String`	`getB37Chr()`
`Integer`	`getB37Pos()`
`Build37ExtendedIlluminaManifestRecord.Flag`	`getFlag()`
`String`	`getLine()`
`htsjdk.variant.variantcontext.Allele`	`getRefAllele()`
`htsjdk.tribble.annotation.Strand`	`getReferenceStrand()`
`String`	`getRsId()`
`String`	`getSnpAlleleA()`
`String`	`getSnpAlleleB()`
`String`	`getSnpRefAllele()`
`Boolean`	`isDupe()`
`Boolean`	`isFail()`
`void`	`setDupe(boolean isDupe)`
`void`	`setRsId(String rsId)`

Methods inherited from class picard.arrays.illumina.IlluminaManifestRecord
getAddressAId, getAddressBId, getAlleleAProbeSeq, getAlleleBProbeSeq, getBeadSetId, getChr, getExpClusters, getGenomeBuild, getHgGenomeBuild, getIlmnId, getIlmnStrand, getIndex, getIntensityOnly, getMajorGenomeBuild, getName, getPloidy, getPosition, getRefStrand, getSnp, getSource, getSourceSeq, getSourceStrand, getSourceVersion, getSpecies, getTopGenomicSeq, isAmbiguous, isIndel, isSnp, setHgGenomeBuild, toString

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Method Detail

getAlleleA

public htsjdk.variant.variantcontext.Allele getAlleleA()

getAlleleB

public htsjdk.variant.variantcontext.Allele getAlleleB()

getRefAllele

public htsjdk.variant.variantcontext.Allele getRefAllele()

getReferenceStrand

public htsjdk.tribble.annotation.Strand getReferenceStrand()

getB37Chr
```
public String getB37Chr()
```

getB37Pos
```
public Integer getB37Pos()
```

getSnpRefAllele
```
public String getSnpRefAllele()
```

getSnpAlleleA
```
public String getSnpAlleleA()
```

getSnpAlleleB
```
public String getSnpAlleleB()
```

getRsId
```
public String getRsId()
```

isFail
```
public Boolean isFail()
```

isDupe
```
public Boolean isDupe()
```

getFlag

public Build37ExtendedIlluminaManifestRecord.Flag getFlag()

setRsId
```
public void setRsId(String rsId)
```

setDupe

public void setDupe(boolean isDupe)

getLine
```
public String getLine()
```
Overrides:

getLine in class IlluminaManifestRecord

Class Build37ExtendedIlluminaManifestRecord

Nested Class Summary

Nested classes/interfaces inherited from class picard.arrays.illumina.IlluminaManifestRecord

Field Summary

Fields inherited from class picard.arrays.illumina.IlluminaManifestRecord

Method Summary

Methods inherited from class picard.arrays.illumina.IlluminaManifestRecord

Methods inherited from class java.lang.Object

Method Detail

getAlleleA

getAlleleB

getRefAllele

getReferenceStrand

getB37Chr

getB37Pos

getSnpRefAllele

getSnpAlleleA

getSnpAlleleB

getRsId

isFail

isDupe

getFlag

setRsId

setDupe

getLine