Package picard.arrays.illumina
Class Build37ExtendedIlluminaManifestRecord
- java.lang.Object
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- picard.arrays.illumina.IlluminaManifestRecord
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- picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
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public class Build37ExtendedIlluminaManifestRecord extends IlluminaManifestRecord
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
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Nested Class Summary
Nested Classes Modifier and Type Class Description protected static class
Build37ExtendedIlluminaManifestRecord.Flag
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Nested classes/interfaces inherited from class picard.arrays.illumina.IlluminaManifestRecord
IlluminaManifestRecord.IlluminaStrand
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Field Summary
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Fields inherited from class picard.arrays.illumina.IlluminaManifestRecord
ILLUMINA_FLAGGED_BAD_CHR
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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)
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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
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Method Detail
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getAlleleA
public htsjdk.variant.variantcontext.Allele getAlleleA()
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getAlleleB
public htsjdk.variant.variantcontext.Allele getAlleleB()
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getRefAllele
public htsjdk.variant.variantcontext.Allele getRefAllele()
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getReferenceStrand
public htsjdk.tribble.annotation.Strand getReferenceStrand()
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getB37Chr
public String getB37Chr()
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getB37Pos
public Integer getB37Pos()
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getSnpRefAllele
public String getSnpRefAllele()
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getSnpAlleleA
public String getSnpAlleleA()
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getSnpAlleleB
public String getSnpAlleleB()
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getRsId
public String getRsId()
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isFail
public Boolean isFail()
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isDupe
public Boolean isDupe()
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getFlag
public Build37ExtendedIlluminaManifestRecord.Flag getFlag()
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setRsId
public void setRsId(String rsId)
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setDupe
public void setDupe(boolean isDupe)
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getLine
public String getLine()
- Overrides:
getLine
in classIlluminaManifestRecord
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