Package picard.arrays.illumina
Class Build37ExtendedIlluminaManifestRecord
- 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()
String
getRsId()
Boolean
isBad()
Boolean
isDupe()
-
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
-
-
-
-
Method Detail
-
getAlleleA
public htsjdk.variant.variantcontext.Allele getAlleleA()
-
getAlleleB
public htsjdk.variant.variantcontext.Allele getAlleleB()
-
getRefAllele
public htsjdk.variant.variantcontext.Allele getRefAllele()
-
getB37Chr
public String getB37Chr()
-
getB37Pos
public Integer getB37Pos()
-
getRsId
public String getRsId()
-
isBad
public Boolean isBad()
-
isDupe
public Boolean isDupe()
-
getFlag
public Build37ExtendedIlluminaManifestRecord.Flag getFlag()
-
getLine
public String getLine()
- Overrides:
getLine
in classIlluminaManifestRecord
-
-