Package picard.arrays.illumina
Class Build37ExtendedIlluminaManifestRecord
java.lang.Object
picard.arrays.illumina.IlluminaManifestRecord
picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionprotected static enum
Nested classes/interfaces inherited from class picard.arrays.illumina.IlluminaManifestRecord
IlluminaManifestRecord.IlluminaStrand
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Field Summary
Fields inherited from class picard.arrays.illumina.IlluminaManifestRecord
ILLUMINA_FLAGGED_BAD_CHR
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Method Summary
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 Details
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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
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getB37Pos
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getSnpRefAllele
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getSnpAlleleA
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getSnpAlleleB
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getRsId
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isFail
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isDupe
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getFlag
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setRsId
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setDupe
public void setDupe(boolean isDupe) -
getLine
- Overrides:
getLine
in classIlluminaManifestRecord
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